M&J breaking up or at least hitting another stumbling block on the friends path is possible and perhaps likely, but I feel very strongly that there is a good chance the throuple relationship can survive and thrive. The only real obstacle in the way of such an ending is DPC themselves if they choose to write this relationship as one that is doomed to fail, because right now it's essentially like DPC has flipped a coin and we're all waiting to see what side it comes down on; a pre-determined, doomed to fail relationship, or one that can work if the right choices are made.
Personally, I just don't see there not being an ending with all 3 of them in a happy relationship together because of what happened in AL. DPC teased a promising threesome relationship and literally killed it, so to do the same again (minus the death, of course) would just be to retread old, and controversial, ground. Relationships in games like BaDIK should always come down to player choice, but if a relationship is doomed to fail no matter what, then that negates the whole choice system and makes it feel like it wasn't worth pursuing the relationship in the first place, which is why the AL is so controversial and it's why DPC shouldn't (and hopefully won't) do that again here.
Even if, on the throuple path, they have a slight falling out, that can still be a dramatic moment where the two girls are at a crossroads as to whether or not this type of relationship can really work, but even then I feel that it can still survive because if players want a relationship with both then they should be allowed that choice and that opportunity.