Do not stop bootstrap instance on error if keep-broken flag is true

Fixes: https://bugs.launchpad.net/bugs/1365772

The --keep-broken flag was added for 1.20.7 and it did stop the environment from being destroyed on a failed bootstrap, but did not stop the bootstrap instance from being stopped. This PR adds in the extra logic to do that.
I'd be inclined to just not call `handleBootstrapError` at all if --keep-broken is specified. There's already a message printed at the top level, I don't think this is adding anything is it?