Maybe it is doing so unconsciously or because it don't know it's a bad thing for you?
Anyway whatever could be explanation this is a subject to fix, having magedoom eye pet is quite unusual (never had one) and I don't see any reason why PC must be punished for having one.

It wasn't a pet by the way, just a randomly generated friendly monster.

Not a bug IMO, because it's an innate ability. Like a monster radiating a chaos aura would still corrupt you, even if generated friendly.

Dervi, I thought about that possible explanation at first, but magedoom eyes very clearly don't drain mana from other friendly spell casters (mana temple is by far the most obvious example).

I'm guessing they simply have no control over their ability. Burb has a valid point, however. While monster spellcasting doesn't follow the same rules as the PC's (monsters have no PP at all), perhaps hostile spellcasters could be affected by this in some way, like reducing the range or power of their spells.