The outlines of a Senate "compromise" on detention have emerged, and it looks like Democrats have agreed to allow military detention in a domestic context with Muslims suspected of terrorism:
Another provision would mandate military detention for people suspected of being "high value" terrorists from Al Qaeda: members of the organization who participated in planning or conducting attacks on the United States. The mandate would exclude United States citizens, and it would allow the secretary of defense to send detainees to the civilian criminal justice system at his discretion.
Military detention on the battlefield is one thing--this provision would extend the "battlefield" to United States soil. With only two exceptions--Jose Padilla and Ali Saleh Kahlah al-Marri--the Bush administration never held domestic terror suspects in military detention. Both of those cases ended with transfers back to the criminal justice system, and both the Obama administration and the Bush administration sought to dodge a confrontation with the Supreme Court over whether or not the U.S. government has the authority to do this. That's because it's hard to square these powers with the plain language of the Constitution--keep in mind the 5th Amendment guarantees due process for "persons," not "citizens." This is an end-run around the Bill of Rights.
It's also not much of a compromise. Currently, Republicans try to exploit fears of terrorism for political gain by arguing that any Muslim suspected of terrorism who is captured on American soil be held in military detention. At the moment, the administration can plausibly argue that military detention for domestic captures was never the policy of the previous administration, so Republican complaints are wholly partisan. Even though the provision gives the SecDef the authority to waive someone into the civilian justice system, Republicans in the future can hammer the administration every time they do so. The difference is that in the future, they can argue that there's a formalized process for keeping such people in military custody, as opposed to demanding the administration radically change the de-facto policy of the last two presidents.