You know who else loves the Hobby Lobby ruling? Al Qaeda….
Gitmo detainees’ lawyers invoke Hobby Lobby decision in court filing

I don’t really doubt the lawyers may have used the ruling in a court filing but I strongly suspect the hysteria is way overblown. They aren’t American citizens and they aren’t technically in America. I’m not sure what the latest developments are but I don’t think they’re in the civilian judicial system. The American Taliban alliance is overestimated.