For some reason, the ambush side missions always tend to revolve around my trying to keep at least some guys alive long enough for me to get off a Face Melter. Otherwise they're just slaughtered. Am I doing something wrong?

This is kind of late reply but I remember avoiding ambush side missions for the very reason and waited until I upgraded my character a little.

Tips in this thread might help.

Exactly. Just wait at your spawn point with all the troops, the moment they clash perform a Face Melter. Solves 90% of all ambushes instantly. You just have to mop up any ranged units after that.

You are generally given much less troops than what the ambush is, so you pretty much have to do it this way.