This has been an issue that has bothered me since the dawn of men.. in warcraft.
it seems that so many classes have pets these days, and it's very confusing and doesn't really "add" anything but just a messy clutter
especially when you're dealing with huge bosses, or you need to see effects on the ground
or even if you just want to know where your actual raid members are, cause who cares where the pets are
Now, Blizzard have already dealt with this issue in Diablo 3.
In Diablo 3, your party members pets are partially invisible.
And i think this kind of solution could work very well in WoW as well.
I'm not sure how hard it would be to implement, but just increasing transparency for anyone who's not pet owner shouldn't be impossible.
Edit: it seems i wasn't very clear, i didn't mean battle-pets. i meant class-specific pets/guardians