I tried applying this script to itself. That was to check if significant uses of '#' were handled properly. The results were, uhhh . . . unfortunate.

1. It stripped the shebang line, which doesn't look exotic at all.
2. It did

   -if ( $us eq "ee" ) { $comm = ';'; } else { $comm = '#'; }
   +if ( $us eq "ee" ) { $comm = ';'; } else { $comm = '
   [download]

   leaving an unclosed quote in the code.
3. It did

   -   die(&pwarn($comm)) if $topline =~ /\#\!.*perl/i ;
   +   die(&pwarn($comm)) if $topline =~ /\
   [download]

   leaving an open regex match.
4. It did

   -     if ( $topline =~ /(\s+)\#\!/ ) {
   +     if ( $topline =~ /(\s+)\
   [download]

   to the same effect.

I think your e can only be applied in the simplest circumstances.

Don't feel too bad, the saying goes, "Only perl can parse Perl." To do this sort of thing properly really does require a parser.