Um, you do know the creator of the guild left it, because it became a beauracratic cesspool right?
I'm not 100% sure, but I think he wanted them dead, because Galerion attacked him (after he became the first lich). If Mannimarco is evil for wanting to stop Arkay, destroy the Mages' Guild, and continue his studies, then what about the Hero of MAN, Pelinial. If Mannimarco is evil, that guy is the epitome of wickedness. Mannimarco isn't good, but Whitestrake is a blind crusader who slaughtered thousands.
So I think battling the Mages' Guild isn't truly evil. They fought first (Galerion, Founder of the Mages' Guild tried to kill him and miserably failed). Mannimarco killed a lot of people, but he didn't do so without justificiation.
Why would he want to attack an institution in retaliation for a guy that long left it wronging him? For that matter, he got his revenge on Galerion long ago. This wasn't about revenge, he wanted to capture Arch-Mage Traven's soul and make him an undead thrall.
The difference between Mannimarco and Pelinal is that Mannimarco orchestrated the attack for his own gain, and he struck at the Mages Guild several times before the Mages Guild actually started fighting back. Pelinal, as insane and bloodthirsty as he was, fought in a war against enemy combatants, enemies that had enslaved the Nedes.
Do we even know why Mannimarco tried to bring down the Mages Guild. (i dont remember)
From what I can gather from the Necromancers' actions and Mannimarco's dialogue, it seems his motivation was to capture Traven's soul in the Colossal Soul Gem and make him a Worm Thrall. Since Traven had banned necromancy, there were many out-of-work necromancers bitter at the Mages Guild, allowing him to gather the forces necessary to carry it out.