I should say that in certain rare instances, mods can "permanently" alter the game (permanently here meaning that you would need to reinstall the game to get rid of the changes). However, this is almost never the case, and when it is it's usually either a) not a good mod or b) explicitly stated. Offhand, the only mods I can think of that would do this are those that have been released for the demo of Far Cry. These mods involve making direct changes to some of the game's core files, so unless you back them up, you're not getting them back without a reinstall of the demo. Even here though, the only reason the mods are like this is because it's a demo. It should not be the case with the full game.
Edit: What I'm trying to say is that you should not let the fear of ruining the original game from preventing you from trying out mods. Mods will almost never alter the original game, especially when talking about a high profile game like BF or Half Life.