This was probably inevitable:
Red Sox Owner John Henry & GM Ben Cherington spoke to Bill James regarding him making public his personal opinions on Joe Paterno. In that call, Mr. James was informed that his comments in no way reflect the opinions or positions of the Red Sox. Because Mr. James is perceived as representative of Red Sox, he was asked to refrain from further public comments on this matter.
That's the organization's official statement, initially delivered via Twitter (yes, it's come to that). It's not clear why James would have been informed that his comments don't reflect official team policy, since he would presumably have known that.
This is all boilerplate, typical cover-your-ass verbiage designed to deflect any criticism away from the club.
I don't imagine that Bill James enjoys being told what he can and can't opine about, but then he's been operating under some restrictions ever since he joined the Red Sox, a decade ago. It's a bitter pill, but I imagine he'll swallow it.