I played through the Mages Guild quest about three times before I read that, and it is quite amazing.

There are reasons we do not know much about Necromancers - we keep on killing them! And if we do not kill them they are killed by their own creations, or any sensible being that comes upon them.

Let's be a bit more precise about Manimarco - the human part of him at least (assuming that he has been split apart into god and human) did not want to kill the mages guild so much as kill the people in the mages guild who wanted to abolish necromancy - fairly reasonable from a necromancer's point of view eh?

Before Traven it appears the majority of Mages Guild senior members were Necromancers or sympathetic to their cause - but they all resigned when they felt Traven went over the top.

Interesting that given what Akatosh has been said to decree re necromancy, but there you go ... Tamriel, will we ever get to the bottom of her - and what shape will we find there?

Given Mannimarco's conflict with the Mages' Guild goes all the way back to Galerion, I think you may be a bit off on him not wanting the whole thing destroyed. It just worked to his advantage that Traven was a [censored] that banned necromancy and gave every necromancer in Cyrodiil an excuse to hate the Guild even more than before, thereby giving Mannimarco his chance to make a move.

Good point about the timeline

Looked at from that perspective - then one might view the Necromancers in the Guild as pawns of Mannimarco - ie he wanted to take it over rather than destroy it?

If all the Guildmasters had combined to kill Traven they would surely have succeeded - instead it was just Mannimarco who fought the hero after Traven sacrificed himself to fill the soulgem. Dang them heroes gets everywhere!

I think that necromancers also worship Molag Bal. In Oblivion, quite a few of their caves (one of them is a misc quest dungeon) have Molag Bal's mini statues in them.
Of course, that does not mean that necromancers are aligned with only one of them. They could serve Mannimarco for Undead powers and Molag Bal for... other powers.

As someone's probably pointed out, it's entirely possible that (GASP) it depends on the individual necromancer. I'll bet not all of them prance around in silly goth cloaks practicing conjuration and shouting Hail Mannis in cookie-cutter Cyrodiilic caves all the time. What's-his-face the Raven comes to mind, as do a lot of other necromancers in Morrowind. They seemed more fond of N'Gasta's little book than anything to do with the King of Worms.