Counter-terraforming is always a good option for Xenocide. But it won't actually remove their pesky ground forces 
Not directly, no.
But by killing the population, you hurt the Xeno's economy and eliminate the reason for them to pay to maintain those fortified GUs.
Assuming you are winning the overall war and their economy continues to decline, eventually they either disband the forces or come out of their fortified position to attack you, right?.
So I suppose you have to decide which route you prefer:
A) Attacking the fortified position with overwhelming numbers, sustaining significant losses, and being done.
B) Stationing (and fortifying) your own defensive forces on the planet until the Xeno units either disband or throw themselves at your dug-in troops.
Route A is faster. Route B is cheaper in terms of units lost, but depending how long it takes and whether you have to build more units to use elsewhere while these units are sitting here, might actually be more expensive in economic terms.
You are probably not going to have much luck with that... as troops are payed in wealth they don't need the local population to be maintained. This is an abstraction mechanic. As long as the troops survive they will stay and defend. The only option is to invade or nuke them from orbit. Even nuking can be quite expensive in terms of resources and you pretty much destroy the planet in terms of using it for your own colonisation.
You can also just ignore and siege it until you have the resources to invade the planet even if that takes time. If your fleet is strong enough that you can maintain a siege there indefinitely you can probably wait for the forces to defeat them on the ground as well which can be a combination of more troops both in terms of quantity and quality.
Remember that if you are the attacker you have the initiative to bring whatever forces is necessary to do the job, as long as you can dominate space that is.
