Hey,
I did the same thing with my Pololu Simple Controller.
Tried to use it on a RC car motor and it fried when the stall current kicked in. One of the MOSFET's (at least I think its a mosfet) in the h-bridge (looks like a h-bridge to me

) went up in flames.. literally in flames and almost set my li-po on fire. Talking to Pololu right now to see if I can get it replaced because they told me that it would work perfectly with my motor. Maybe you should try the same? Contact them via
[email protected], they got back to me within 2 hours at 9PM EST. They ask a lot of questions so be prepared

.
I'd suggest looking at the 4 ICs hidden under the Cap, one of those is what fried for me.