Support for the --kill-nailguns option was inadvertently removed, this puts it back.

The kill-nailguns flag was being read through old_options.cleanup_nailguns

Also updated the nailgun timeout logic to try and pinpoint transient errors in CI if it
happens again.

This reverts the change at https://rbcommons.com/s/twitter/r/1345/ which is redundant with this one (and not as effective.)

Testing Done:
CI Passed.

Bugs closed: 803

Reviewed at https://rbcommons.com/s/twitter/r/1352/