You're missing the part that came before. The one where you've deserved every inch of whatever Coulson's done to you. What happened to Agent 33 was regrettable, but you would have done far worse to her.

[That's how he reconciles it. He was with Bobbi for every step of her recovery. They've talked through her lingering guilt, even as she supported him through his grief.

He doesn't answer the other lingering question.. He might have brought up Kara as a distraction away from Jemma.]