Thanks for info, I see the same behavior here.
Regarding to question about removing only one association, this isn't possible in ORMD2 because of different MN handling in ORMD2. Original ORMD handles MN as two separate associations joined by one MN element. But ORMD2 handles MN as standalone object with connection to owner/inverse entity and MN entity. So removing only one side isn't possible.
Probably would be possible to left MN table undeleted after removing MN association, but I'm not sure if this is better behavior than removing it.