points out, qr//
is meant to quote a pattern, not an entire substitution. If you want to pass in literal substitutions, rather than just patterns, then just eval
at a different point:
eval "\$text =~ $pattern";
By the way, ikegami suggested using (?i:) in place of a string-based eval. Since such evals are always a cause for concern, and should be a cause for terror when run on user-provided input, are you sure that you considered the alternative properly before making your decision?
If you're not happy with the inability of a (?i:)-type solution to handle substitutions, then you can probably just offer --search and --replace --by flags so that the user can specify directly what he or she wants.