No, he escapes anyway.

Or to be more precise, he escapes with or without your help because he's still got to have his climactic battle with Vanus Galerion and the Order of the Lamp later and then appear as the King of Worms in TES Daggerfall and thanks to the Dragobreak get to become the Necromancers Moon in addition to attacking the TES Oblivion Mages Guild out of a very, very long grudge.

Mannimarco has a LOT of plot armor for future installments.

But if you want to roleplay that you are guilty, go right ahead. I prefer to muse upon the nature of unavoidable fate.

Except for the weak depiction in ESO and maybe Oblivion(which is up to debate if it is the real one) Mannimarco is actually a very strong magician who survived for couple thousand years now. I don't know why they made him so dumb in ESO but when you see how he acts in Daggerfall, a cunning influential Necromancer operating hidden, you might think what happenend in ESO then... He always tried to achieve godhood which he actually did in daggerfall then so i assume it was a attempt from his younger years.

The plan he has as actually not bad because of his superior knowledge about soul gems he knew that the amulet of kings is a soulgem which has the power to prison daedric gods which is crazy and only 5 of the mightiest persons of this time could stop him and presumably he would have killed them if molag bal did not intervene.

To the question of the topic: I assume he escaped at the point when we did weaken molag bal in the main quest when we defeat him. I bet he lost a lot of power for a short duration when he was wounded so there might be a window for escaping. Nontheless he will escape somehow eventually

As Necromancer you actually can be agent of Mannimarco, Hail Black Worm!

Just imagine, Mannimarco need Amulet of Kings, but Sai Sahan is too sturdy in his willpower even Duchess of Anguish can't break him,
https://en.uesp.net/wiki/Lore:The_Unbreakable_Redguard
So Mannimarco searched for another way, sacrifice own Necromancer to make him double agent, so he can achieve trust of Sai Sahan.
Mannimarco hide your soul gem from Molag Bal as it was described in his memos
https://en.uesp.net/wiki/Online:On_Soul_Shriven
And allowed you to run from The Wailing Prison with Prophet didn't you think that's escape was too easy from such high guarded facility? Molag Bal switched his attention from, miserable soulshriven slave to escaping Prophet, so Mannimarco scheme worked as planned.

We saw many times that's he used his necromancers as fodder and disposable material, so his word to you are honest, so you understand his loss of pity for you, since you are just asset in his scheme, but for you, perhaps before sacrifice, Mannimarco himself can be much more, leader, teacher, even god if all goes as he planed.

Maybe its even your journal from previous life https://en.uesp.net/wiki/Online:Necromancer's_Journal

When you are done your mission and Mannimarco get Amulet of Kings you are no longer needed, and he cheated you with return of your soul too since your soul gem become much more powerful and precious, what are ***, so you can kick his ass in righteous fury to get back your soul gem, but Molag Bal was greater schemer than Mannimarco.
Perhaps from this time you are released that's Molag Bal is the greatest threat and your Master ultimately failed in his achieving of godhood. So you honestly allied with companions against Prince especially when he snatched Mannimarco and actually have your soul.

From this side releasing Mannimarco can be your last deed for your former master, as you still have certain feelings for him that's are not only anger, perhaps its apology for him since because of you he failed and your anger broken master plan what Mannimarco weaved all those times, he honestly did not understand your actions, that's why he answered in such manner.
Perhaps releasing Mannimarco that's last sparks of loyalty, or that's companions changed your alignment to neutral or good.