Obama, when asked if he would appoint Republicans to serve in his cabinet, said that he would.
Chuck Hagel is mentioned specifically in the article; as I've said before I think he will probably be offered something. However, while I agree with Obama that "national security in particular should be nonpartisan" (quoting the NYT's paraphrase there), I don't think it makes sense, if you are going to replace Robert Gates immediately, for a Democrat to appoint a Republican to replace a Republican to head DoD. There are plenty of qualified Democrats.
As for the specific question of whether Gates should be kept on, I see the logic. But I also agree with Yglesias that the main question here is not whether Gates has done a good job but whether Gates would enthusiastically support Obama's plans for Iraq and Afghanistan. That's a call that Obama will have to make after sitting down with Gates and talking things over with him. Whatever Gates' qualifications for the job, if he's not willing to do what the President wants him to do, he's out.
And that's as it should be, partisanship aside.