Obviously there was blowback, but the belief that we were wrong to arm the mujahadeen is itself grievously wrong. The Soviet disaster in Afghanistan does not happen without the Stingers and without the disaster the Soviet Union does not fall either as it did or when it did.
Asking if it was wrong to arm the mujas is like asking if it was wrong to send the Sovbiets 3/4 million trucks, 8500 Sherman tanks. 7,000 P39 & P 40 aircraft to help them fight their Great Patriotic War against the Nazis. BTW we sent aid BEFORE we were at war. What was the result? 50 years on the nuclear mousetrap until Ronald Reagan, Bill Casey brought down the house. Arming the mujas was no small part in that effort.
It's very possible that some power we are enlisting to help us with al Queda will come back to bite us in the future. But since we can't see the future we can only deal with one enemy ata time.