My computer can run Unity 3D comfortably, and I don't really want Unity 2D as a fallback. Can I remove it without breaking my system?
Of Course you can, just use
sudo apt-get remove unity-2d.
My Two Cents:
This will not modify your Unity 3d as they are 2 different packages. But in my opinion failing of your default graphics card and id your alternate card(if any) wont work with 3d right away, you can use unity 2d. you can use
apt-get again but why go through the waste of time? Besides it only takes 205KB of disk space.
AFAIK Unity 2D and 3D are different packages. So it should not broke anything!