They could "know" there "idealistic, good-guy scientists" all they want, but in the end there NOT the US Government. Do you really think they would leave the rebuilding to a group that wasn't affiliated with the US Government no matter how good there intentions? They don't know who the teams are, there history or the Projects long term goals and plans. So putting some Green Berets under to keep an eye on the Morrow Teams would be a plan and probably one of several but the only one that got further than the planning stages.
As for using the Morrow Teams wake up signals it makes kind of sense, the US Government may not know when the Morrow Teams plan to wake up, just that they do so using the Teams signal solves two problems, the US Government doesn't have to come up with there own timetable, they just piggyback on the Morrow timetable and they don't have to develop a system to check to see if the Morrow Teams are awake or not.
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