Your second and third point is confused. The foundation for the government's belief they can deport Khalil is not the Alien Enemies Act (which is what I assume you mean, as there is no Alien and Seditions Act-the term "Alien and Seditions Acts" refers to four separate acts, one of which is the Alien Enemies Act), it's the Immigration and Nationality Act, the same basis Trump tried to use for Executive Order 13769. More specifically, I think they're using 8 U.S.C. § 1227(a)(4)(C)(i).
That said, the government is absolutely using the Alien Enemies Act to round up people and send them to El Salvador.
>If these people don't have rights to free speech and due process then nobody does.
So this is an interesting legal question because non-citizens definitely do not have complete free speech protections, but the border of where their speech is protected vs unprotected is not entirely clear. It's not true that if they don't, nobody does - it is absolutely clear that citizens of the United States do have rights to free speech and due process. That has been established many times.