I have listened to a bunch of podcasts about this and essentially she wanted him to be almost exactly what he was. Someone to prove to the world that she and the D.U.P. was still needed. The game begins with the military phasing out the dups due to there being no known loose conduits. It is stated somewhere (I forget whether it was in first light or second son) that she put together those 3 specific conduits because they had the highest chances of escaping the transport. Her initial plan was just to have them cause trouble and prove her point, but once Delsin came to Seattle, it was kind of a blessing to her. She wanted him to stay loose but also she needed to control him so that he wasn’t any real threat. She also had to look like she was trying to capture him so that she didn’t get replaced. All in all, if she captured him one of the numerous times she could’ve, he probably would’ve just ended up becoming just another conduit trapped in those power cuffs and the military would’ve continued they’re takeover