You need to be worried about the bench being too strong, not the press. The press, as a function of the movement, stabilizes muscles on both sides of the shoulder. So as you get strong at press you balance the shoulder and therefore cannot become "imbalanced" while pressing. The bench press on the other hand only works the anterior shoulder and thus sets people up for an imbalanced strengthening of the shoulder leading to issues. Perhaps improper form could lead to pain in the shoulders from pressing, but if done correctly they should not be causing pain. This is why for people with bad shoulders Rip recommends eliminating the bench entirely and only doing the Press.
Either way if you want to get the bench up that is fine, but I would still keep some pressing just to make sure you do not develop an imbalance. The Thrusters will act as some overhead work, just make sure you are not cheating the overhead part of the thruster