Mike38, a couple of thoughts:
One immediate difference between a citizen and a non-citizen is that the non-citizen can potentially be deported for relatively minor infractions.
As a corollary to that thought, the non-citizen has to regularly re-apply to remain in the US. I have a non-citizen friend who is married to a US citizen, and he has to do regular interviews with US immigrations officers to renew his green card and maintain his ability to work in the US. It's possible, though unlikely, that he could have either or both permissions denied by some bureaucrat.
The next thought is that you say you have no problem with "legal immigration." That's what we are discussing - the law in question would bar (or the court case might allow) lawful resident aliens (like my friend) to obtain NM permits. (My friend is in FL, so it wouldn't really apply to him - though he does hold a FL CCW.)
The case has nothing to do with allowing illegal aliens to obtain permits.