From the publicity surrounding her nomination - it is not that clear that she should have been nominated, but that isn't my call. And it should have not been the call of McCain. Rice said: “If nominated, I am now convinced that the confirmation process would be lengthy, disruptive and costly to you and to our most pressing national and international priorities,” [Susan Rice withdraws name to replace Clinton].
I noted in another post that she might have gotten her comeuppance. The picture painted of her wasn't that flattering. But unless there was something very wrong with her, like some criminal conduct or major breach of ethics, any president should be able to have, or at least nominate, who he or she feels is right for the job.
The secretary of state performance reflects on the president more than on the secretary. Sure the Senate ought to have a say - but McCain and friends want to speak for the Senate. [See Susan Rice, the Senate and Angry Mobs].
It is personal for McCain and friends, Libya was just an excuse. The Republicans are still upset that Obama was elected and re-elected. It is doubtful that any Obama's nominations will get far in his second term. More of the gridlock.