To prevent rust from forming around drilled holes, I'd recommend a dabbing some POR-15 rust proof coating on the bare metal edges/local drilled hole area. You can get it online at
www.por15.com
I've used this stuff before to restore a few rusty parts, such as some rust spots on my rear subframe, and to protect and put a hard coating on some critical wear areas on my car's underside - frame rails and hardpoints for jacks & jack stand were getting beat up by usage. The stuff is a bit expensive, but it works exceptionally well and you get what you pay for. For a small job like your holes, they have a starter kit for about $20 that has everything you'll need to clean/prep/coat a small area.