The evidence is the reading that Gorman's placement isn't a coincidence, because Burke's plan falls apart if it is (as evidenced by how quickly Hicks shuts him down).
Likewise, Burke's apparent control (to a point) over Bishop is further evidence that he (and by proxy, WY) is able to exert control over the USCM, otherwise you'd expect Bishop to shut Burke down too if Burke's requests violate quarantine procedures.
Side note, Ripley's "smuggle the embryos, sabotage the cryotubes" theory is pretty much fabricated out of thin air - perhaps he intended to fully disclose that Ripley and Newt had aliens inside them and would let WY hold them in quarantine until they can do something about it.
Parker suggests the same thing in the first movie with Kane ("Why don't they freeze him?"), implying that merely freezing him is an acceptable way of getting the obvious facehugger through quarantine.
Burke obviously planned to openly transport the facehuggers and thought he could get away with it, he tells Bishop to do it. Face hugging Ripley is a (f**ked up) way to keep her from objecting.