There are a couple of ways around this, though it is always a useful tactic that makes life hard for your opponent.
Firstly, bear in mind that you can shoot most MCs without cover in this situation. MCs may or may not be your priority targets but if you have guys with lascannon s and the like, fire them at the MCs.
Killing the gaunts is an option, though they will be cheap and take a lot of shots to remove. Putting a few flamer templates on the forest is a good way to reduce their numbers, though you will often be charged by other stuff afterwards. Thunderfire cannons, incendiary rounds from whirlwinds or sternguard and Tau airbursting frag launchers can all help.
If you play chaos, lash the gaunts somewhere and you will be find. Other armies can attempt to replicate this by charging the gaunts in their bit of cover. The ones in the open have to bundle towards the charging unit and will quickly get out of the way. Unfortunately though, they will still be there for one shooting phase at least.