Avery didn't want to hurt her boyfriend but it looked like she was going to have to in order to get away without explaining her plan. Which she couldn't do because that sort of carelessness was how villains got caught. He would be on the lookout for her stealing insulin again if he knew what she was doing was a regular occurrence.
If her plans remained a secret, Mercury might assume she had a one-time purpose for it. She really hoped that was the case. She didn't want to shut down her insulin delivery system.
"I'm really sorry about this," Avery mumbled as she finally managed to gain the upper hand by climbing on top of him, grabbing the box, and using him as a springboard instead of a building to make her next jump.