If I was just making the rifle for myself,,Id soft solder a close fitting 12L14 steel pin thru the hole. Trim it off to the oct flats on the outside and lap the bore out to take any offending bit of matl away inside.
(If a customers gun or one built for sale on speculation, of course the bbl would be replaced.)
It'll save the bbl for shooting purposes, you won't notice any difference in performance and the oops will still be a reminder for the next project. It's called learning, everyone has their storys to tell.
You can always come back and change the bbl, use the punctured one for pistol bbls, ect later on. But for now, avoid the extra cash outlay, that can sour an otherwise fun project.
Learn from it and make something of it.
Put a mark on the bottom to indicate the flaw if you want to avoid anyone from not knowing should the rifle pass on to someone else w/o your consent.
Just my thoughts..keepin it low cost to keep it fun.