I also think it preferable to have NO guns on board at all, and I was also thinking of the damage to the Aircraft, and/or decompression.
However saw a very interesting segment on one of the cable news channels the other day, all about these sky marshals in the USA. Showed the weapons they use, and their ammunition, I cannot remember the technical term for it, but it is special ammunition that will not penetrate anything much more dense than a person. So although it will still very effectively wound and/or kill a hijacker, it will NOT penetrate the aircraft skin or even windows etc.