Does distributed propulsion create unwanted lift at cruise speeds, requiring a negative angle of attack?
The fundamental way distributed propulsion adds extra lift is by blowing additional air over the wings. This is a direct thrust-to-lift conversion.

If you produce less thrust, you produce less lift with this arrangement. 

So, no, you don't go to a negative AoA to counteract the excess lift produced by running all of your motors at full power. You never produce that excess lift in the first place. This involves running your wing propulsors at reduced power, and if you have lift-assist propulsors, such as blown flaps, turning them off altogether.