I'm not convinced it actually made sense, but I think what they were going for: Cohaagen didn't want to kill him because he was a super spy. Locking him up would mean he'd never lead them to the resistance, and he'd never do that willingly. Giving him a false life in the colony means that he's out in the open for Jessica Biel to come find him and lead him back to the resistance HQ. Giving him a fake wife and fake best friend means they can monitor him around the clock in case he's contacted by the resistance. And wiping his memory means that the resistance will accept him without suspecting he's turned or anything.

Not what you'd call a foolproof plan. But then this is the tactical genius who put his entire robot army on the same elevator and announced to everybody that he was about to launch an invasion.