No Gmod does not interfere with Hl2 in anyway. Gmod has it's own folders for everything it needs, and gets hl2 stuff from the GCFs which it can't edit just read.
The great thing about Steam is that everything is stored inside read-only GCFs. If your game installation is screwed up, you can just delete the folder inside your steamapps\<steam user name> and run the game again. Now you have a fresh install!