These rough guards ticked me off in the past in the Hubso I decided to waste them with a well placed frag grenade upon opening the door and then wasting them with my 10mm SMG. I saved the Initiate but now what? I realized now it is a BoS quest so when I reach the point if I join them will I still get my reward or is it forfeited because I did the quest too early?

I am not sure, but I think you will get an option to tell the BoS that you already saved the recruit when you pick up the quest... or the recruit tells them that you were their savior and thus they skip straight to the reward.

Oh okay I guess that sounds logical. Thanks!