The radiation damage is problematic, but, well, habitats and automated mines should cover that problem. And if they don't it's time to break out the high power spinal beam cannons so you only have to deal with the dust.
Radiation affects production, regardless of whether you use automated mines or the population is in orbital habitats. That is true in VB6 as well. The only mining method that is unaffected is orbital miners, but they have a planetary size limitation in C#. So you can massively irradiate the planet to kill the ground troops, as long as you don't plan to use the surface of the planet afterwards.
You can use energy weapons, but they only shoot at one soldier at once, rather than the 150 per 9-point warhead, and your base chance to hit before fortification and terrain is 7% compared to 100% for a nuke. They are much more useful in supporting ground troops than trying to pick off individual soldiers from orbit. You could theoretically do it given enough time and maintenance supplies (weapons malfunction in C#), but I doubt it will be economically viable. Again, this assumes the ground forces aren't shooting back.
C# mechanics are designed to make ground combat a real option, even the preferred option in many cases. You can still choose to wipe out ground forces and populations from a distance but that option is much more costly than before in economic and environmental terms. With some ground forces vs naval forces, it might not even be a viable option.
As for deliberately creating a nuclear winter to kill all the trees, that is a creative solution but you still have the environmental problems as a result. BTW Forested Mountain survives all the way down to -50C. It would be easier and cheaper to send in your own ground forces, which is all the new rules are trying to achieve.
Finally, you reminded me that I forgot to include terrain fortification modifiers in my original example. The infantry should have been at 6.75 fortify (3x inherent * 2.25 for terrain), so only 3 infantry would have been killed per warhead, not 7. 3270 9-strength warheads would have been needed, not 1450. I agree that that at some point, the fornication and to-hit modifiers would change, but it is still actually worse than my original example.