This is code lifted some time ago from an older version of Filter::Simple (by the Damian). I use it whenever I need to make substituions in code-like-strings, but I want to make sure I don't changes things inside quotes.

quote_protector.pl

sub whatever
{
    use Text::Balanced qw< extract_multiple extract_delimited >;

    my ($string) = @_;

    # this replaces all quoted strings with placeholders
    my @quoted_strings;
    $string = join('', map { ref $_ ? scalar((push @quoted_strings, $_), "{Q$#quoted_strings}") : $_ }
        extract_multiple($string,
        [  
            { SQ => sub { extract_delimited($_[0], q{'}, '', q{'}) } },
            { DQ => sub { extract_delimited($_[0], q{"}, '', q{"}) } },
            qr/[^'"]+/,
        ])
    );

    # ...
    # (do whatever you want to $string)
    # ...

    # and this replaces the placeholders with the original quoted strings
    $string =~ s/{Q(\d+)}/${$quoted_strings[$1]}/g;

    return $string;
}