IMHO, since it went through an arsenal rebuild and that stock was installed then, it's just as correct as the stock it was originally built with. The rifle was rebuilt while in service and returned to service as such, so it's an honorable veteran no matter what changes were made to it. I'd leave it as-is. It's not like the stock was sawed-off by some Bubba or replaced with an aftermarket stock after it was mustered out of service.
It's still a USGI rifle and a veteran, I'd honor it as such. I have a 1943 Inland M1 carbine like that, has an M2 stock on it from a rebuild, and most of the finish is gone off the metal. I could restore it to pristine condition, but I like it as it is, scars, scrapes, gouges and all. It's a vet of God Only Knows What, and it deserves my respect. It gets to go everywhere with me in my truck, in a USGI canvas M1 Carbine carry case, resting comfortably on the back seat.