Silicone isn't bad as long as it's neutral cure (ask any girl that's been enhanced).
Sikaflex seems to be the most popular sealer for cars. Clean around the holes on both sides, apply rust-inhibiting paint all the way and once this dries, apply some sikaflex to the hole and put a grommet through it. The grommet will help withstand the pressure of the water if you go that deep. Give the sikaflex a day or two to dry before you go windscreen-deep in anything.