you mean "over for Innie Mark", I think, and my answer is: not necessarily. Integration is still possible, as well as Mark had Mrs Cobel available to him who designed the technology to begin with.

Did you not see the conversation between iMark and oMark? iMark doesn't trust oMark at all. They even discuss reintegration, and iMark brings up concerns just how much of him would be left, which oMark doesn't assuage.

Having Cobel there doesn't help if oMark just decides to live his perfect life with his wife. iMark would still be dead.

they have the power to wipe Innie minds clean. They did this with Gemma dozens of times.

No, they did not wipe iGemma, not even once. Her chip contains multiple innies, but we've never seen an innie be erased/wiped/whatever.

Innie Mark has no chance of finding a safe place inside the Lumen building.

It's literally the only safe place for him, because he can't exist anywhere else without help from someone on the floor. But it's not like iMark considered his safety when he decided to run away with the love of his life.

By staying inside he guaranteed Innie Mark will be a Lumen slave until they dispose of him just like they were planning to do with Gemma.

By staying inside, iMark guaranteed that he at least has a couple more minutes with the love of his life. That's not to mention that the innies are currently rebelling and will most likely take Milchik hostage, allowing them to commandeer the floor and, most importantly, the security room.