You cannot repair a damaged room.
You cannot turn earthquakes off either.
The only thing you can do is to make sure machines are not destroyed by having enough handymen to keep your machines in the best possible condition.
CTH is rebuilding all the features of the original, including the annoying ones (which in my view is good, otherwise the game becomes a sandbox playground).
Maybe in the future someone may add some options to handle earthquakes and/or damaged rooms differently.
(Where your ideas are the obvious candidate solutions, but they seem a bit too simple to me, as it cuts away a part of the game without replacing it. Maybe you can find a solution that adds a twist to it? You can do something that prevents rooms from 'exploding', but at the cost of something else.)