Kanno pretty much nailed my response before I even made it, including Gilgamesh initial thought. Nice.

Fujin and Raijin aren't what I'd call villians, but I suppose you could argue they were around the same as the likes of Rude, Reno, Elena, Tsung, etc. If you do include them, then yeah, they're just loyal, sorta like Arbok and Wheezing with Team Rocket. They love their masters but they know their masters are bad. But they don't do bad things unless their masters order them to.