The solution to this is disconnect the solar panel when the alternator is running so the controller doesn't function. This can be easily done by putting a switch in the positive wire leading from the solar panel to the controller. Alternatively, you could put in relay (closed when no powered) on this wire and wire it so the relay is open when the engine is running and closed when it is not.
There is another very good reason to put a switch in the panel to controller wire. The smart regulator reads the battery charge condition and sets the output of the alternator accordingly. If the solar panel is producing power, the regulator will see the net of the battery charge plus the panel output and thus may prematurely put the alternator in float mode. this will result in getting limited performance out of that big expensive alternator.