I've been mulling this, and I'm just not sure if Scully would go along with this plan. Part of my problem is that we have basically no evidence from canon of how she feels about giving up William. Could she get this desperate, or feel sufficiently guilty about having taken Mulder's son from him to feel like she has to go along with it? Because of the characterization problems of s9, it's very hard to understand where Scully is going into the post-Truth period.