i reckon if it were a good idea, guitarists everywhere would be doing it.
the technical, electrical issue is that with such a low output from the pickups, the amp has to draw upon its power to, well, amplify it. by using both channels (and i believe you'll also change the impedance which each amp input sees), you're just increasing the power demands from the amp.
do you know the 4 ohm and 8 ohm power output ratings for the amp?