That is odd...

#!/usr/bin/perl

$string = "a\@b.c\n";
$string =~ s#\Qa@b.c\E#email-address#g;
print $string;

$string2 = "a\@b.c\n";
$string2 =~ s#a\@b\.c#email-address#g;
print $string2;

$string3 = "a\@b.c\n";
$qm3 = quotemeta('a@b.c');
$string3 =~ s#$qm3#email-address#g;
print $string3;
[download]

Output:

a@b.c
email-address
email-address
[download]

So it seems that method won't work correctly. Perhaps another Monk can enlighten.

Corion suggests that \Q$var\E should work as normal; perhaps change the line that reads:
$code .= "s{\\Q$in\\E}{$out}g"
to read:
$code .= "\$var=quotemeta q{$in}; s{\$var}{$out}g"
for all to be well with the world. And it appears to, as well.

Update:D'oh, messed up the replacement line,fixed
Update:Corion once again points out that the reason for this is because @b gets interpolated before \Q takes effect. I should have realized this was the case.