As far as I understand it, the objection would be if
- you were simultaneously a key person in Nix, like a release manager
- your company officially sponsored events that associated Nix with military
- several of your employees were active contributors to core parts of Nix
I think the last one might not even be a big issue, or at least it might not blow up.Surely, the usage of Nix in any domain is a free choice. You can't really police that anyways.
And to clarify above, there was no "contributors of this company" dynamic to the outrage.
"jobs" are things which come and go, not a lot of people are will to burn their personal image for a [potentially] uncaring company. And I'm certainly not one of them either.