Gordon had been deliberately targeting Sam and wanted him dead. Those were repeated personal attacks, and I don't blame Sam for taking them personally. Even so, Sam wasn't as completely remorseless in his killing of Gordon as Mark-of-Cain!Dean was in killing whichever of the vampires got the short straw at the end. Dean is usually only like that when something is going very wrong in his head, so it's no surprise Sam noticed and mentioned it.