Yglesias discusses the SecDef’s magnanimous position on his soon-to-be-replaced subordinates:
To provide some background and context, you need to understand that a lot of these guys were never Gates’ people anyway.
Gates and Donald Rumsfeld had some pretty different ideas about a lot of stuff, but when Gates joined the Bush administration he wasn’t given the opportunity to clean house, fire everyone, and bring his own people on board. Since he’s been in office for a couple of years there’s been some turnover since that time, but still a guy like Edelman has always been a Cheney/Rumsfeld guy who happens to be serving as one of Gates’ top deputies, not a Gates guy who Gates is desperate to hang on to. In fact, I think we can be fairly certain that Gates’ views are closer to those of a moderate Democrat like Flournoy than to Edelman. So whether or not to get rid of people probably wasn’t a bone of contention between Gates and the transition. What needs to be negotiated isn’t whether or not some of these folks need to go, it’s who to replace them with.