Like many people commented here already I don't believe Mara will be the one to betray us.
Even in alternate timelines she has always been a steadfast ally (even if her methods are questionable at times)
I think like you mentioned it might be more likely Clovis has some backup plan to betray us and become a disciple of the Witness in his grand scheme to become human's savior / emperor.
English
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Yeah I pegged him from the start as a surprise Disciple. I don't know why we keep him around, we should yank him off Europa and shove him in a deep and dark bunker under the City and let the Splicers and Rasputin play with him. His knowledge is invaluable, he is not. Let them peel him apart and extract the useful bits.
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Yea… I threw out a crazy idea just to see if anyone agreed I do lean more towards Clovis betraying us