Unless you fancy a reinstall come patch day, keep a copy of the original files handy (i just rename them gibberish before copying cracks across.)
I've also known some games to refuse to play multiplayer if the MD5sum of the .exe's differ, if you want to avoid the patching and *possible tho unlikely* MP issues I'd suggest using CP emulation in the forms of Mini-Images, Full Images, or loaders such as GameJackal/GameJack.
These however are not without their disadvantages, namely that you need extra hdd space for extra programs/images, that running the game is no longer a case of just clicking the icon, and that you still have to suffer invasive, unreliable, buggy CP systems
