Well, as Paulyoung has said, water shouldn't be a problem, as windows have drainage built into them, and are designed to drain any water away to the outside.
Depending on whether the glazing beads are on the inside or outside will determine whether or not security is an issue, but to be quite honest, if you can just pull the gasket out, it makes no difference anyway.
So if the only issue is the appearance, you could always buy a tube of black silicone sealant, and whizz around the edge to make it look okay. The 'trick' is to run low-tack masking tape (decorators from Wilko) around the glass and the frame, leaving just a few millimeters gap where the gasket would go. Then run the sealant around, smooth it flat with a wet forefinger, and then slowly & carefully pull the masking tape off, which should leave you with nice neat straight edges to the sealant.
But before you start, you may need to push something into the gap left by the gasket to stop the glass from moving about. Suckersticks usually does it
Hope you get it sorted okay, if not, post back.