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Usually, you can't alter too much the scripted NPC stories; At least until you actually complete their "act". 

You may try to force some "bugs" by using cheats and editing their likes, inclinations and such, so they dislike everything about the other one, but I suggest doing a hard save before you try anything.

(+1)

I more meant like if there will be a future route that lets you break them up pre act

If there is, the devs haven't dropped any hints about it. Until you hear otherwise, it's best to assume not