@sanity: I've been playing as Aragon, and things are slowly chugging along. I've been having a standing army nearish to the force limit with maintenance turned down as you suggested, and haven't had any bad effects in terms of rebels etc.
With religious conversion, you will probably have to pass some national decisions that help rebalance your tolerance for heretics / missionary effectiveness, or take up national ideas that help with this. After Protestantism comes along for instance, Aragon got a lot of national decisions to either start to counter Protestants or allow for more religious tolerance
There is also a national idea that allows at its first tier to get another diplomat; quite a few different national idea trees allow for this at different stages. And yes, if you remove a diplomat mid-annexation, I believe it does reset the timer
I have not found a way to improve your own nations opinion of another nation, which is something I really would like to do...
Hope this helps?!