Was a lot of the functionality of Quake done in QuakeC or was that scripting language added for the sole purpose of allowing for mods to the game?.

I think scripting languages are a very bad idea for the core functionality of a game and I see no benefit to them. If its done after you have nailed down all your core mechanics and just want to add mod support for things such as player created maps then I think that's fine.

That means that a scripting language should only be added towards the very end of a project. Adding it towards the beginning when you don't even know your core mechanics yet seems crazy to me since I see no benefit to it.