1st of all don't regret taking the time during the HS season. Bottom line, it shouldn't hurt his recruiting. I'm not sure what's going on, but it is a good thing you are taking care of it now. A kid on my son's HS team had a shoulder issue all throughout his junior year. He put off having anything done to it until the season was over and I think it really hurt him. Because he waited, he missed all summer and fall and was just getting back senior season. Because he didn't play summer or fall, he had very limited options and is now not playing in college. He should have taken care of his arm right at the beginning of his junior year and been ready for fall ball, camps and showcases to have a shot.
I think you are doing the right thing and you should be fine, especially if he'll be ready by summer. That is when the big action takes place anyway.