According to one of the RPG sourcebooks (and I'm sorry, I forget which one exactly at the moment, but I'm thinking "Magic & Mayhem") the Titans put the Well of Eternity there to be a source of nourishment to Azeroth. It's why there's magic in nearly everything, and when you get right down to it, that means all magical energies are arcane in origin. The problem with arcane energy causing corruption isn't the energy itself... it's elves using it in an unintended way. Not to hate on elves, just that if you follow the lore it does go back to them. Bending the energy to your own will is what results in corruption, and that's what they did. Then the high elves taught humans to do it that way (because they knew no other way, of course) in exchange for help against the trolls. And the Kirin Tor still does it that way today. (Someone should probably ask Richard Knaak why Krasus has never been concerned enough about Rhonin to give him a little nudge toward the truth about that.) Runes, sigils, marks, etc channel the energy through naturally present paths, rather than bending the energy to the casters will. That's why arcane corruption isn't a result.

So, the Titans put the Well there... they didn't find it. And the Well itself isn't a source of corruption. Elven hubris is.