Here is a quite contrary appreciation of Robert Gates from Ambassador (ret.) Jack Matlock, writing from personal experience.
Goodman's comments are more slander than truth. When Gates was deputy DCI, I was the "action officer" in the NSC on Soviet affairs and thus the funnel through which CIA reporting on the USSR went to the president. Gates never censored it, though his own judgments at times differed both from those of some analysts and from those of us on the policy-making side. He always qualified his judgments and presented both sides of the arguments.
Mel was pushed aside not because he refused to "tailor" the intelligence to suit the White House, but because he insisted on making derogatory remarks about U.S. policy--which he clearly did not understand and which, in any case is not supposed to be an intel function--and also because he does not draft very well. (There are passages in his "biography" of Shevardnadze that wouldn't pass muster in a freshman essay in English Composition 101.) He has made a career in his retirement of going after Gates, often quite stupidly.
At times, Gates' views (and those of Bill Casey) differed from mine and Bud McFarlane's and George Shultz's. For a long time Gates was convinced that Gorbachev was simply trying to make the Soviet Union more powerful in order to carry out its traditional aims. But he always made clear that not everyone in the agency agreed and he sent forward the interpretations of those who differed from him. As for the president and his "team," we made up our own minds, based more on our direct contacts with Gorbachev, Shevardnadze, et al. The agency as a whole was not close enough to the situation to be helpful; our embassy in Moscow was spot on regarding every key question--and those were the reports that guided US policy in the latter years of the Reagan presidency--and subsequently with Bush I.
When Gates was on the NSC, he was very level headed and judicious. He is not an ideologue and definitely not a neocon. (You don't see many around the Pentagon these days do you?) He is a good leader who does insist on accountability--as he did with aberrant analysis like Goodman and more recently with the Air Force brass. Friends who teach at Texas A&M sing his praises as a university leader.
If Gates is asked to stay on a DOD for a while, I have no doubt he will try to execute the policy the president decides with skill and good judgment. But the president will have to make the really tough decisions.
Recently Gates has been a stronger voice for building up and funding the Foreign Service adequately than even the Secretary of State.