The reason why Dewey only deploys the Asset instead of multiple high level agents like the previous movies is because he only trusts the Asset to kill the CIA's own agents if that is what it takes to neutralize Bourne.
Hirsch's decision in Ultimatum to take Bourne through the training facility and help him recover his memories now has added depth - as revealed in this movie, Hirsch believed that Bourne was a patriot at heart who could eventually be convinced to be brought back to the program. That's probably what he was trying to accomplish.
We only get to know of Dewey now because he is the smartest of them all: The moment Jason Bourne went rogue in Identity, he went underground, cutting off anything that could link him to Treadstone/Blackbriar/LARX/whatever assassination program the CIA has in play. He takes power only after Pamela Landy is disgraced and the public made to believe that the assassination programs are legit programs.
Bourne in this movie seems more comfortable with the use of lethal force as compared to previous films. He kills (or seemingly kills) three people in this movie - Christian Dassault, Craig Jeffers and the Asset. Four, if you count Malcolm Smith, who he essentially used as a human shield. That's a pretty huge body-count for a Bourne film. But it makes sense when you consider the fact that Bourne is, in many ways, fundamentally a different person in this movie. He now has all his memories back. Unlike the amnesiac Bourne of the previous movies, this Bourne is every bit the former soldier and trained CIA assassin who has no qualms about killing when necessary.
While a high bodycount, it makes sense in that 3 of the four were attacking Bourne, and the fourth guy is clearly meant to be a cathartic moment, so Bourne primarily stays to his no killing rule.
