I can't tell if your question is referring to the technical aspect of replacing the keys, or to general pros and cons of doing that. But one thing you might want to consider is keyboard shortcuts if you use them. Copy and Paste, Save, Select All, etc are easy to use on a QWERTY keyboard, but might not be on whatever layout you intend to switch to.
Of course, getting used to an uncommon keyboard layout will also mean that you will have trouble writing on other people's QWERTY keyboards – only if you often interact with others and their computers though.
As for the process of replacing the keys: there shouldn't be any problems. People do it all the time and there are plenty of guides and video guides out there to show you how to do it. For example: MacBook Pro/PowerBook Keyboard Replacement (Part 1 of 3) or How To: Replace or Clean your MacBook, MacBook Pro, or MacBook Air Keyboard Keys
Search on YouTube for more if you don't like these.