That's really horrible bro...But, like you said...things could be worse...
You already know all this and I'd like to re-iterate it for anyone else that might not know. When drilling, it's essential to have a RUNNING FLOW of cool water. The debris from the drilling has to be washed away or there might be and uneven-ness in the drilling. You should also drill at a medium speed.
That's all my opinion of course. I've drilled about maybe 6 holes in glass in my whole life so I'm NOT the expert here. LOL
As far as re-installing the new piece...that's cake-walk. Just make sure you completely removed the old silicone from the old glass and thouroughly clean the old glass and new piece with alcohol. Then, apply ample amounts of fresh silicone to the clean glass and place the new piece into place.
Then, apply another small line of silicone to the corners and run your finger up and down the corner to spread in out and to push it into the seam. Trick: use painter's masking tape to create perfectly straight lines. Simply mask off where you don't want the silicone. That's show you'll get a professional looking finish ;)
If you use alcohol to keep your finger wet, youll get a better spread and get it off your finger easier.
Take your time and don't think you're dong anything wrong. The only concern I'd have is whether or not the new piece is exactly the same thickness :D
So sorry to hear about that again :(