The Showtime series's second season saw Estes call off the planned murder of Brody at the last minute, only to die himself in a suicide bombing at CIA headquarters.
In an interview with The Huffington Post, Harewood said Estes was ultimately "justified" in targeting Brody for death.
"I think [Estes] was fully justified in trying to get rid of Brody, even though all the ladies don't think that's the case," Harewood explained. "I think he had to go."
He continued: "I mean, this was a guy who put on a suicide vest. This was a guy who was prepared to blow up half the American administration - including me!"
Brody denied any involvement in the CIA bombing in Homeland's season finale, but the creators have said they want audiences to have a lingering doubt about the ex-Congressman's motives.
Reflecting on his two seasons on Homeland, Harewood admitted that Estes was not an easy character to understand.
"I struggled in the first season to figure out who he was," the actor commented. "I would write myself a backstory, and then you'd get a script that would completely contradict that backstory.
"Just as I'd begin to like him, he'd do something which was a real pain and I'd have to go, 'F**k, okay'."
Homeland executive producer Alex Gansa recently hinted that season three will feature a much "smaller" story.