I prefer Missile Launchers in infantry squads as they are easy to mount on 25mm bases!
The weapons however for me are fairly equal, statistically the Missile Launcher is better against MEQs, plus it can instakill T4 and touch heavier armour.
Statistically the Autocannon has the edge against anything with worse than a 3+ save and vehicles with AV12 or lower.
So really the question is: what is the main role of your infantry? The main role of my infantry is to fire at marines and not have pain-in-the-ass 60mm bases, so they are equipped with missile launchers!
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