There's a difference between "wrong" and "possibly unwise."
IMHO, it is not morally wrong to take a mass-produced rifle you've purchased with your own money, and you lawfully own, and modify it (legally) to your heart's content, IMHO.
HOWEVER, it may not always be the wisest use of the rifle, and if you screw up something that may be valuable someday, you may end up kicking yourself like the guy who carved, cut, welded, and tubbed his 1957 Bel Air in the early '80s because he thought it would be cool to have a "Pro Street" car with three foot wide tires, a powder-coated roll cage, wheelie bars, and shag carpet that would barely run twelves in the quarter, because that car is now much less desirable than the unmodified car.
However, I can find little fault with the guys who irreversibly modded a 1969 Camaro to make this work of art, which is arguably more desirable than the original car:
http://www.bigredcamaro.com/newsite/
As to rifles, if I had a rack-grade M44, I'd probably have no qualms about modifying it for a scope. But my Finn M39, I'd go with a no-gunsmith mount (like a Millett) rather than permanently modifying it.
I'd probably be OK with refinishing the stock to protect it, though, just as I'd be OK with repainting a 1957 Chevy rather than keeping the "pristine" faded paint with the rust spots showing through.