In r22303 I have committed patches which address -- and may even resolve! -- the issues discussed in this ticket. Default behavior is largely unchanged, i.e., if a configuration step fails, Configure.pl proceeds to the next step. But now, at the end of configuration, you get a printout of the steps that failed and a caution about proceeding further.
If that's not sufficient, with the --fatal-step option you can now designate one or more steps (comma-delimited list) as causing configuration to halt upon step failure. And if *that's* not sufficient, you can run Configure.pl with the --fatal option, whereupon the failure of *any* configuration step will cause all configuration to halt.