That's what Sen. Feinstein reports (linked to and quoted by TPMmuckraker: "We assured the administration that Colonel Davis would not be asked about open and pending cases. But we were told simply that Colonel Davis was active duty military, and because he was active duty military, they could issue an order he had to follow." (Recall that Col. Davis has publicly criticized the operation of the current military tribunal system, and resigned his chief prosecutor post because of his views.)
I'm sure Col. Davis does have to follow his commanding officers' orders; I can't speak to whether the Senate has subpoena powers over such officers, but to my knowledge he hasn't been subpoenaed. But I can say that, based on the facts as reported by Sen. Feinstein, this seems like a very bad move on the Pentagon's part, both politically and from a policy perspective.
The Congressional oversight power, though it can often be abused, is quite necessary in such situations, especially when the judiciary is likely to give considerable deference to the executive (as it in considerable measure does, though some think it should give still more deference). It seems to me that for the executive to block testimony before Congress that might shed light on how the system operates, and whether it has flaws that jeopardize both defendants' rights and the system's accuracy and efficiency as a warfighting tool, both looks bad and is bad.
Thanks to Victor Steinbok for the pointer.