Those who oppose Obama, as well as a majority of supporters, have had issues with who he has been selecting for departments. His choice of John Brennan as CIA Director might be the last straw for some supporters who don't think he has been upholding his promises. Although Brennan can be seen as someone who will get the job done, Democrats will not be able to forget his support of torture during George W. Bush's terms.
Brennan as CIA Director could be seen as a surprising choice, and I'm sure some people will disapprove of it, and by that, I mean Obama. However, Obama will not be tarnished by Brennan's past indiscretions, if only because the public is short sighted and has a very small attention span. A majority of people probably couldn't even tell you why some think that Brennan could ruin Obama's reputation in the first place.
President Obama has made some bad choices concerning who places in any department. I do not think John Brennan will hurt Obama's reputation. Even though he supported torture during George W Bush's term, I do not think that Obama's reputation will hurt in any way. Most people will not remember about the Gulf War, so Obama will not be harmed!
While it is easy to see how John Brennan becoming CIA Director could potentially cause harm to Obama's reputation among both those of his own party and of the Republicans due to his support of torture throughout George W. Bush's terms, in the long run his effectiveness at his job and the practicality of his knowledge will win out and Obama's reputation will be fine.