Currently having fun trying to get reputation up with the Templar without (permanently) crashing my reputation with anyone else. It's a bit tricky (and I had to do some save-scumming just to figure out the rules for how reputation from crusades worked), but makes a good endgame goal.
The trick is that you need to keep your reputation high enough that the penalty from the crusade doesn't push you over -75 (and thank goodness it doesn't penalize your reputation with pirates!), which generally means spending the second half of each crusade hunting bounties instead of continuing to kill stuff in the crusaded system. Which, in turn, makes it even slower to get rep with the Templar, but so be it. (Slower once because you aren't spending the whole crusade duration contributing; slower twice because you have to wait for crusades to hit systems where you'll be able to get rep back in time; the Hegemony works well, because they've got presence in enough other systems that there are almost always bounties available; something like the Sindrian Diktat I'd just leave alone and let the crusade go off without my help.)
...Of course, once I have that Templar reputation, I'm going to buy a bunch of stuff and then turn on them. But it's probably still easier than capturing their ships; either I got really bad luck, or they just always explode now.