And, it's a bit pie in the sky to think that everyone will read that history the same way. Better, istm, to deal with it head on than to ask people to ignore it (which is what it sometimes seems some here are asking people to do).
Honestly...I haven't seen many Catholics here who say, "Oh ignore all that...just trust me, it's not what you think." I've seen plenty who have spent time and energy trying to put historical quotes that have been conveniently plucked out, back into their historical context. I've seen attempts to explain our POV on certain events, not to excuse them, but again to put them back in a proper context. I've seen exaggerations be challenged, and I've even seen admissions that the Church does indeed have blemishes in her past that should not be ignored or swept under the rug.
From the other side, I've seen faux history being presented, attempts at correcting it ignored on the grounds that anything coming from a Catholic concerning history can't be trusted and must be untrue, venom spewed in return to attempts at explanation, insults, etc. (Alongside plenty of other non-Catholics who tried to minimize that and stop any unfairness, which I greatly appreciate!
So...I guess I haven't seen many Catholics here, or non-Catholics of the non-anti-Catholic variety, saying "ignore that." And you know what...that's kind of what I found of (knowledgeable) Catholics in general when I first started actually looking at history for myself and not getting it from anti-Catholic sources alone. Now, with my anti-Catholic ears prior to that, if I heard someone putting it back in historical context I immediately thought, "Ugh...trying to justify those atrocities and ignore history." But, when I actually looked at what they were saying and considered it, I found, to my surprise, I was the one ignoring stuff. What they were saying could largely be backed up with secular history sources.
That's actually the section of history I've been reading lately, from a few different sources. Some of information (or perhaps misinformation in some cases) is not to be laid only at the feet of Catholic critics (Protestants, et al.) though, as there are quite a few more "secular" historians who do quite a number as well. Catholic apologists are quick to distance the Catholic church from the execution of John Huss. Secular sources say he was condemned at the Counsel of Constance because of his Wycliffian teachings, etc. and that the counsel had him burned at the stake to prove their own orthodoxy. Apologists say it was really just the civil authorities that executed him. Pope JP II said the church made a mistake in having him executed...which sounds like an admission that it wasn't really just the civil authorities behind his death, at least to me.
I share that example to simply say that our problem with history is that at this distance, it's hard to be very trustworthy of either side's accounting. Personally, it leaves me often .
I can understand that, but I think the best thing is to read both sides, try to find unbiased sources whenever possible, read those too, and see which makes the most sense, and fits the most facts. I really do believe it's possible to gather enough reliable evidence to support one side or another, or see if they can fit together, and to just use the old noggin and think critically about this stuff with the available info.
For instance, your example...I've not studied it in depth and don't remember many details, but going purely on what you said it sounds to me like the secular side is acknowledging the close ties Church and State had at the time (which they did...which MOST Churches and states did as a given), while the apologists are trying to put something that sounds shocking to our modern ears (we who hold up the separation of Church and State as a fundamental principal) back into context, to remind people that it wasn't just the Catholics that were tied up with the state, that's just how stuff was done back then! And then JPII is saying, regardless of what was commonly done at the time, we now realize executing people (whether it's the state or church that does it) for heresy is not a good thing, and we apologize for the part we played in it in this specific case, and others. (Cue all the other groups who did the same thing for their own apology...) That apology is NOT admitting the often-held idea that it was just the Catholic Church doing that kind of thing, nor is that what most (fair and unbiased) secular sources are saying (they're usually just reporting the facts), and that is all that most of the apologists are trying to point out, that it was a human problem and not a uniquely Catholic one. So...they kind of all fit together, you just have to see what it is each one is trying to say, and what angle they're coming from.
The biggest problem, in my experience, occurs when people have strong internal bias, and don't want to believe certain things, and do want to believe other certain things to justify their bias. (And that, of course, can happen on either side.) What happens then is talking past each other...one side assumes they know what they other side is saying, and they don't actually listen. The respond with some non sequitor because they didn't listen, and they don't think they need to listen because they already know.
For instance, for specifically anti-Catholic bias, people point fingers at the violence and such of times past, and often blame it on the Catholic Church, because conveniently there were no protestants around to blame it on! But the problem was not a specifically Catholic one...it was usually a HUMAN one. Look at the times and culture of the crusades and inquisition, and you'll find, not a largely peaceful society with a mean awful Catholic hierarchy trying to cause trouble in its midst, but a generally often violent society, with contemporary human beings who lived in that society and were used to it who happen to also be Catholic. Was there corruption in the Church? Yes! Just like there was corruption in any organization of the day. Were bad things done in the name of religion? Yes! Just like bad things were done in the name of the king, or society, or family, or any other human organization.
Now, the problem is plenty of things have been exaggerated, taken out of context, misunderstood, blame has been misapplied, and so on and so forth, and it's often hard and exhausting to have to wade through all of that to get to the factual truth, and then begin to put it back in historical context. Again, that's not to justify any wrong that was done, but to more accurately be able to see what wrong was actually done and why, and to consider the surrounding culture. Now, try doing this with someone who wants to believe the worst and who wants to blame the Catholics for everything, and they will typically stop listening before they start and assume you're just trying to excuse/justify/ignore history, then accuse you of such for trying to explain without having taken the time to consider what you said at all, because they "already know" you're just going to deny any wrongdoing on behalf of the Catholic Church...because that's what Catholics do.
It's a vicious circle.
It's really quite frustrating, especially when you have to start from scratch with each new person who brings out the same old arguments based on exaggerations and faux history.
Anyway...don't know where I'm going with all that, lol, I'll just stop there!