As far as the theoretical term is concerned, regular expressions with backreferences are not regular expressions. The power that backreferences add comes at great cost: in the worst case, the best known implementations require exponential search algorithms, like the one Perl uses. Perl (and the other languages) could not now remove backreference support, of course.
Cox then proposes a hybrid engine that can be quicker when capture groups aren't needed. TCL has this sort of hybrid implementation, http://wiki.tcl.tk/396. It's worst case performance won't be big-O better than Perl's for pathological cases that require backtracking.
If P no more or less equals NP today than in 2001, the article's conclusion has not lost correctness.