For a small flying wing, can two motors with different speeds replace the ailerons?
First thing first:
I think you mean yaw not roll. See Yaw definition

If you actually mean roll, then the answer is no.

If you mean yaw; then the answer is yes.
However it is impractical for two reasons: 

1) Engines, especially jets but also propellers have a latency when speeding up and down. This will make it impractical, and might create pilote induced oscillations. 
Electrics motors are more reactive, but so far they have yet to be commonly used in aviation.

2) Redundancy. If one engine fail.... you have to shut down the second engine, and you lost yaw control.