I don't use mouse broadcasting for that exact reason and I don't know of any solution for it either. In fact, the only reason I added mouse broadcasting was due to popular demand by the people that I gave my synergy keyboard broadcasting modification to.

My technique is to have 4 characters on auto-follow and keyboard broadcasting almost always on. I then unbind movement keys on all but the primary character. If I need to micro-manage one of the characters I just mouse over to that window and use the mouse to control the character and when I'm done I move back.