I stitch patches on all the time - I have a Zo bag and sew directly through the inner vinyl. The tiny little holes are not going to let a bunch of water in.

Most likely you will be sewing a patch onto the flap of your bag anyway, yes? Since the flap covers the main pouch you will still have another layer of protection. If anything, tape will come off the inside - if you are really concerned, I would use Super Glue to seal over the inside stitch.

Edit - Oh yeah, using a thimble really helps a lot and will save you from an inevitable finger-puncture...