There's a body health separate to total health?
I thought it was just total health and head health?
Anyway, going for headshots when you can is better for gameplay/strategy/doing your part for the team, and while playing the game either way, the limiting factor towards leveling up is your stalker kills, so it's a fool's errand to avoid headshots.
If you absolutely must get commando damage, bodyshot the last bloat of a wave or something instead of being a drag on the team all the time.
Hmm, I have a 0 experience commando on my new second account; maybe I'll try leveling that up for a while trying to use just headshots and see if damage ever becomes more important to leveling than stalker kills.
Edit: I just did a little experiment. I might not like the result, but here it is. Starting with zero experience, I bullpup headshotted a normal clot, he died, I ran for a bit, check my stats, and I had 99 damage. I bullpup bodyshot another normal clot, ran for a bit, checked my stats again, and I had 229 damage.
So the bodyshot kill yielded 30% more damage in this case, which seems indicative that bodyshot exp > greater than headshot exp in general. Dang. But still, what I said about stalkers applies, probably, and what i said about not being a drag on the team definitely applies. Go for headshots, please.