Was Doakes a Killer?

Okay, so Dexter didn't technically “kill” Doakes; it was only by proxy. Doakes perished in a fiery explosion due to a blaze set by Lila.

Why did Doakes hate Dexter?

Season one

Doakes hates Dexter Morgan; he is the only person in Dexter's life who can see through his mask of normality. ... Ultimately, Doakes realizes that Dexter is withholding vital information on the Ice Truck Killer case, to the point that he is driven to physically attack him, only for Dexter to expertly fight back.

Why did they kill off Doakes?

In a 2007 interview with the Pittsburgh Post-Gazette, the show's executive producers stated Doakes was too good not to kill. Further, they insisted that another season of Doakes chasing Dexter would be “redundant and would diminish both their characters' intelligence.”