So it's been a while since of finished the agent story so I'm a bit fuzzy, but didn't I completely clear my name from all databases? If so why, when I do endgame content, are the quest givers calling me a good asset to the Empire and a huge help etc when they shouldn't even know who I am? Is there some sort of reason behind it or just discrepancy in the story and the endgame content?

I don't remember your name being erased from the databases, but there was a lot of awesome stuff happening during the last mission so I might have overlooked it. I would hazard to guess that even though your name had been erased, people in high up places would still remember your reputation, especially Darth Marr.

You had a great reputation once, the people who were around then aren't going to just forget it.