I don't really think this would be viable for a number of reasons. The first is, obviously, the close links between the USMC and the USN when it comes to logistics and transportation. DoS doesn't have the capability to handle this, and the USMC doesn't have the organic capability. Second, you run into the question of budget and funding. DoS doesn't have the clout DoD does.
Aside from that, there are other factors that would end up clouding the process. In the "old days" DoS was oriented more towards preserving and even expanding the position of the United States (most of the USMC's involvements while "troops of the Department of State" had at least veiled empire-building designs), whereas today I would argue that DoS is more political in nature and oriented towards objectives that may not be as conducive to USMC involvement as they were "back then." Putting the USMC under State might also, to foreign eyes, confirm their supposed role as America's Imperial Police.
The bonuses you mention are indeed compelling, and certainly the Marines are best suited both by experience and temperament to work with State, but I think that a wholesale move would be in no one's best interests. A system of fixed unit rotations might work better.
Another thing to consider is the impact that pulling the Marines out of DoD might have on DoD itself. No matter how much the other services posture and protest, it's still easier to get a MEU on scene if there's a crisis. They are the best structured, trained, and positioned to respond quickly to an emergency. Losing that capability would require the Army to venture into areas that they have had little recent experience with (with some exceptions, mostly within the light division community) and have historically shown little inclination to deal with. The Air Force certainly can't pick up the slack here; tribesmen and others don't tend to be impressed by F-22s and the massive use of airpower is often counterproductive.
Interesting idea, though. Maybe USAID should merge more with the USMC, or some sort of combined/joint task grouping could be developed along those lines.
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