Yeah, necromancers get a lot of crap that was probably taken to the extreme, but they aren't exactly "gray". http://www.uesp.net/wiki/Oblivion:Falcar was sending new members that wanted recommendations on suicide missions for being upset. Necromancers do use black soul gems, though I admit this is a weak argument since many others use soul gems on like everything else. Burning down a guild hall was pretty brutal. And just recently since I got back into Oblivion yet again, I really started taking a good look around and noticed that a corpse, not a zombie, was upside-down on a rope hands tied behind back with a lot of pieces ripped off in a necromancer's cave. Since necromancers aren't that accepted into the public anymore I'm pretty sure they're getting their bodies from innocents now rather than being able to use prisoners and traitors like before. Even then, experimenting inhumanely on people is pretty dark stuff, regardless of what they've done.
Dunno why I felt like adding my two cents, but the point I want to make is that I wouldn't go so far as to label the Mages Guild evil, but I will agree that they have problems or moral issues that they aren't realizing, or maybe they do and don't care which would be worse. There are members that join the guild for a good cause or believe they're doing something good for all (Arch-Mage Traven banning necromancy for example, and since I haven't delved deeply into this matter I won't say whether I agree or not), and there are those who are bitter, selfish, greedy, power-hungry, and/or even "evil". And necromancers aren't all sunshine and rainbows either.
And they shouldn't be. They're necromancers. They have a rep to keep. :chaos: