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.