You have two options when it comes to removing geometries/not drawing them.
1. Remove the geometry from the physics simulator in the collision by doing this:
private void OnCollision(geom geomA, geom geomB, ContactList list)
Calling .Dispose() on a body or geometry will mark it as disposed. Once the physics simulator traverse the list of geometries and bodies, it will automatically remove the disposed objects and clean up after them.
2. Disable the body and stop drawing it.
When you detect the collision you simply disable the body. You can set Body.Enabled = false and it will not be updated in the physics engine. If you ever need the body again, you simply enable it again. In your drawing code you need to check if the body
is enabled before drawing it. The advantage of disabling it instead of removing it is that you can reuse the body and geometry. You can also save some resources using this method if you respawn geometries (like bullets out of a gun).