The ref $proto || $proto idiom is not bad in and of itself. It's bad when it's tossed in around blindly without documentation because it suggests that perhaps the programmer is unaware of the intention. If, however, the programmer has a reason for this idiom and documents this reason (even if only through tests), then I'm less concerned. For example, one person mentioned that they frequently use factory classes to pass objects to other modules than then call new on instances of those objects to spawn further objects. This can be a reasonable approach and if it's documented and tested, no problem.
As with anything in Perl (or even life), I would hate to automatically declare anything wholly without merit (with the possible exception of bell peppers -- they're just gross), so I'd argue that this idiom has it's place so long as someone knows why they've put it there.
Of course, in the interest of full disclosure, I'm the guy who submitted the patch that had the ref $proto || $proto code mostly removed from the latest perldocs.