I hope she becomes president eventually...i think she is a very smart, powerful woman who could show women could be a leader as well as men can.Almost forgot to answer your question! No, she can still run for president.
If Obama decides to run in the next election (which tends to be the case) than his party will support him and no one will try and run against him (the vast majority of the time). so while no being Secretary of State doesn't mean she can't run for president it's highly unlikely that she will do so in the next election.