According to the license

However: the code and assets may not be used in commercial mods, mods for other
games, other games, other non-game projects, or any commercial projects.

I am writing a open source (in the future open source, currently WIP so closed source), non commercial web GUI for this mod (a 3D web gui where user can control the turtle and the world around him). I have used the turtle model in that app. Is it okay to do so or does it volatile the license?

I think you'll have more luck asking on the relicense issue on CC:Tweaked (sucessor of this mod) repository:

cc-tweaked/CC-Tweaked#1339