If its seems fine without it I dont see how it can hurt it. It sounds like your stalling from running pig rich. My bov releases from pressure alteration, so if I give it gas and let off the gas it opens the bov (even if its in vacuum) and releases air. It doesnt cause my car to stall but causes a temp. rich condtion and occasionally it bogs a little bit. Im almost sure the problem is related to running rich when backing off the throttle. If its fine without the vacuum line hooked up and working (which is strange) I say leave it off. If it causes any problems just hook it back up... However that means the boost is forcing it open, maybe its a sign the bov is not in great shape (just guessing, I know nothing about your bov).
