Though some factions appear to coded to attack you at least early on, I believe(and stand to be corrected) that maintaining good relations and reputation will allow you to avoid wars you don't want.

There are several threads on reputation, but things like exterminating drive it down a lot.

I don't think you can be friends with everyone for ever so choose your enemies as well as your friends, but as a catholic faction I'd suggest paying tribute( say 100x100 florins) to maintain relations with other catholics which look threatening.

You also choose the assasin/spy covert war style against your enemies rather all out blitskrieg, slower but just as much fun.

I'd also recommend Lands to Conquer mod which fixes a lot of annoyances and makes a few things more sensible and logical.