From someone who uses the Perpendicular snap almost daily I don't see how you can accuse that of being the culprit of everything - I'd lay the blame on shoddy autocad operators.
Why not just turn it off? I work with pretty much all OSnaps turned off, and invoke the one I need with a three-letter combination (PER=perpendicular). If it's that painful for you to keep it on, it sounds like the best option. At least I have never come across a way to change the priorities of OSnap.