Why not?

while( <FILE> ) {
  push @file2, $1 if m/^confederation-as-router:\W+\d\W+\d+\W(?!.*cr\d
++)$/;
}
[download]

Although I bet you could improve on that further... reducing the .* to something more specific.

Update: I missed the negation in that. oops. I've added it to my regex. Thanks runrig and Tye for pointing that out to me. (For those who missed it, I forgot the ?!)