The lower BS of the Scouts makes a one-shot weapon such as the missile launcher seem less attractive to me. More importantly, a squad full of snipers will be shooting at a) infantry or b) monstrous creatures., because shooting at a tank would be wasting the snipers' shots. Vs. infantry, the heavy bolter is better hands down. Vs. monstrous creatures, the heavy bolter is about as good as the missile launcher (lower AP, but is almost guaranteed to wound). So my vote is for the heavy bolter.
That said, my suggestion would be not to run scouts at all unless you're fielding a big unit of 10. The lower BS really screws them over.