I'd support either of those scenarios!Making an exception to my "do not write for free" rule:
1) MJ and Paul were never intimate, they just co-raised the chains. After all, they were the only 4 "people" on the planet, it makes sense to form a society of sorts. She is still with Paul because they both know Wayep still wants Peter dead but because she was tricked to accept Rabin's chains of her own free will, she's the only one who still has a psychic connection to Wayep and knows Wayep would use her to find Peter (Wayep is defined as trickster god, twisting the fine print about free will is something he would like; also Wayep seems to need an anchor to find Peter, can't find him on his own or else he would have had his revenge long before Dead Language). She doesn't want to distract Peter by having him worried about her all the time and she can't be with him because she is still an antenna for Wayep, hence why she told Peter it was too difficult to work with him in a recent ASM. Jackpot is her trying to learn how to use the device for the final showdown with Wayep, who Paul knows from the previous showdown on his planet is still recovering and regaining his corporeal form but will return. They are both trying to prevent the acopolypse on Paul's world from happening in 616 (twist would be Paul is just biding his time until Wayep recovers and then he is planning to take his father's place). Yes, she should tell Peter but she's still suffering from PTS from her ordeal; she feels she brought this on herself and she's the one who should solve it (see: MUH RESPONSIBILITY!!1! from ASM 9); she's reverting to old habits by putting on a happy face and running away from the people she cares the most about.
2) MJ has known all along the kids weren't real and Paul is an unreliable narrator, and she and Paul have never been intimate but she's happy to dangle him along to keep him sweet. By accepting Rabin's chains and Paul's largesse, she is keeping herself and Peter alive. She uses her considerable acting skills to pretend to be happy with Paul - even to Paul's face - even though it breaks her heart to hurt Peter because she knows if Peter dies, the apocolypse she foresaw in the vision given to her by Rabin would occur. She's with Paul because once she accepted the kids - she wasn't going to let even fake kids suffer in the dystopian world and besides, they gave her a buffer from Paul - she learned the chains couldn't be broken even when Rabin took the kids away (which he actually did to punish his wayward son, for wanting to keep MJ instead of sacrificing her). So she's keeping an eye on Paul and his potential to turn evil again much like how Peter said he was working for Norman to keep an eye on him. That's why MJ placates Paul whenever he brings up how sorry he is that his dad made him commit planet murder, to keep him docile and unsuspecting. That's also why she pretended to be bad actress while Paul was listening in on her fight with Francine, so Paul wouldn't suspect she is actually giving the acting performance of her life. She got him to modify the Jackpot device so she could learn how to use it without killing herself, with the full intention of using it at full power, regardless of the cost to her, to ensure she can protect Peter if and when a final showdown occurs. She doesn't tell Peter because she knows Paul has the ability to listen in on her and see through her eyes when he wants thanks to the chains - hence why he listens in on her and sees through her eyes when she's Jackpot - and she doesn't want to tip her hand.
Not the best, but that's off the top of my head.