Lemmy, first thing you need to about church is that if you research techs that are proscribed, they will send their troops in your labs ONLY. And they will keep sending them as long as they have troops, transports or you loose the offending tech (by loosing all your labs or striking it).
AFAIK there is a simple way to use any tech in the game without having to worry about church invading your labs. You simply have to build cities all around your labs. Since church doesn't invade anything else (if you are not in war with them) they won't be able to attack your labs. It worked for me.
Also there was a bug (even in 1.4 Version) that makes all the new proscribed techs reset every time you save - exit - enter - load game.
Hope this helps.