Here is what Melev says about my acro and cap growing together:
I would leave it and see what it does.
I bet you could extract the plug from the M. capricornis and not even damage it. The lower coral would look funny, as it won't be touching any rock at that point.
There's no reason to kill off any part. Even if there was some left on there, it may grow out a different direction later.
So, for now I think I'll leave it and see what happens.