ediff-grab-mouse

ediff-grab-mouse is a variable defined in `ediff-wind.el'.
Its value is

t

Documentation:
If t, Ediff will always grab the mouse and put it in the control frame.
If 'maybe, Ediff will do it sometimes, but not after operations that require
relatively long time. If nil, the mouse will be entirely user's
responsibility.

You can customize this variable.