The only time I can recall Hunter ever being civil to the IA was in the bar on Nar Shadaa when you first meet the SIS Team. After that, it's D*ck City, and I leveled both male and female Imperial Agent.
IMHO, Hunter is one of the best antagonists I've ever run across in a story, hands down. Most people playing have very visceral reactions to him. I literally was shaking my fist at some of the crap he pulled/said. But I won't spoil anything for you, as your opinion of him may or may not drastically change at the end of Act III