Your idea isn't bad. As a matter of fact, it is the one of the main combat mechanics of Fallout 3. The idea that guns can't fit in RPGs was populated by the fact that most designers either didn't create their RPGs in a setting where guns would fit, or they couldn't find a way to meld it seamlessly with the rest of the weapon mechanics in the game. You could make it so that each weapon type has a certain set of attributes, and guns would be able to do piercing damage and were very weak. Final Fantasy XII is a good example where guns make sense -- you can have different types of ammunition, each with stat effects and bonuses.
Hope you find a method that works for you.