Depending on how abrupt your changes are gonna be, you don't need o decompile the model at all. All model textures are stored seperately to the model in the GCF files. Here's an example:
Let's say you want to change the skin of one of the human rebel models in HL2. All you'd need to do is open the Source Materials GCF, go to hl2/materials/models/Humans/ and then choose the appropriate folder and model. From here, you can extract the VTF file for whatever model you wish to edit and then edit it (you'll need to convert the file to something that image editing programs can open, that or get the VTF plugin for Photoshop which I believe is floating around).
Once you've done the editing, you'll need to put the vtf file in the correct place. For the above example, it'd be something like "Steam/SteamApps/username/half-life 2/hl2/materials/models/Humans/etc etc". Basically, anything that has the same file name as a file in the GCF (and in the correct place) will replace the file in the GCF. So if you have "skin.vtf" in the "materials/example" folder in the GCF and "skin.vtf" in the "materials/example" folder in the HL2 folder, HL2 will use the one in the folder, not the one in the GCF.
You can basically make colour changes to the skins and other minor stuff (adding bits of extra detail and whatnot) as the skin will re-map itself in the exact same way it always did.