Although a Templar, Haythem Kenway was a dignified man and didn't show the tyrannical behavior (forced labor and use of fear) that most Templars flaunted except for maybe when he beat down Benjamin Church.
Charles Lee was the biggest, most realistic kiss-*** (and frankly the ugliest with worst haircut villain in the series) I've ever seen in a game in the beginning. He harassed a very young Native American child and insulted his people, so he was clearly an ignorant bigot.
Where as Haythem clearly respected the Native Americans and treated them as equals and had noble qualities like when he called for fighting with honor on the Providence, returning a chest to its "rightful owner" and no more.
Seriously, what qualities did Haythem see in Charles Lee that made him go through all the trouble and dying for ruining Connor's attempt at killing Lee? Such a waste...a lot more could have been done with Haythem and Connor, but that's another story.