I believe the flights to El Salvador were private charters, not military. The earlier flights to Guantanamo would have been military, but even that isn’t clearly & blatantly illegal. Trump claimed legal authority based on an existing legal precedent (I forget which), and since military pilots are not lawyers they followed those orders. The flights stopped in part because of all the legal challenges in court (but also due to costs and other legal issues).

If anything, when ordered to fly these people to Guantanamo, the military probably turned to their JAG officers, who are lawyers, to ensure they weren’t illegal. They likely would have said the flights should go until the courts ruled on the matter.