Glenn Greenwald asks
The reasons seem obvious to me.
Pentagon fears that in working in official capacity with Wikileaks, it may:
(A) legitimize Wikileaks,
(B) undermine their case against the Wikileaks if its was ever bought to the court, and
(C) Through cooperation additional information such as context, reason for redactions would be revealed to Wikileaks, leading to potentially more embarrassment.
Its all sums up to reflect the negative kind of establishment instinct towards outsiders.
New York Times is probably siding with Pentagon against Wikileaks, to preserve their relationship, and fend off the threatening challenger in Wikileaks and their business model.
To the contrary, I actually think that it would be a great competitive advantage for the NTY to establish a regular working relationship with Wikileaks, few news media organization have such access.