I will wait for the whole story before judging. I suspect one of the questions is did he provide material support for Hamas, but did not disclose it when he got his LPR status (AOS or consular processing)? I have no idea if he did, I understand he worked with UNRWA for some time, and that agency had or has murky ties to Hamas. As to violating his first amendment rights, I understand some of those Columbia protests were quite violent, and damaging to property, etc. I guess if you are OK with Jan. 6th rioters being punished for violating the Capitol grounds/building (I am), then someone leading a protest that breaks laws, damages property, or violates the rights of others can be prosecuted and punished.
As I said, time will tell how this goes, but I suspect there is a reason Mr. Khalil was the 1st targeted individual. Whether that reason is valid remains to be seen.