To answer you:

1. Patch 1.1 tones them down somewhat, but they are still a bit uber, to avoid them you HAVE to keep very good papal relations, that or play as a non-Catholic faction, otherwise he WILL send inquisitors after you.

2. no, and theirs no code for this as far as i know so your probably not going to see this put in prior to an expansion. It was simply never intended to be possible and as a result theirs no way to add it.

3. Not yet but their are plenty of mods that fix the issue and a CA fix is due i the next patch, the problem is fixing it screws balance over quite badly TBH, so they have a lot of testing to do at their end.

If the devs haven't fixed these issues, is there a player made mod out there that might?
See my Signature for my ProblemFixerV1.13.

Another well known mod that will that you could use instead is Lusted LTC. You can find that here.

Both Lusted and My mods fix a bug that results in characters having less starting piety than they should, thus they are now more Inquisitor resistant than they where. they both also fix the billmen issue and an issue with Shields.

You WILL need Patch 1.1 for both of these mods however as the trait changes do not work correctly otherwise.