A simple experiment under Windows 7 shows that, as others have noted, entering a backslash via STDIN should not be a problem:

c:\@Work\Perl>perl -wMstrict -le
"chomp(my $pw = <>);
 print qq{>>$pw<<};
"
r;OFTaf#a2Mt9d\1
>>r;OFTaf#a2Mt9d\1<<
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Once you have the string in a variable, there should be no further problem: as shown in the example above, Perl does not re-interpolate interpolated strings.

Can you provide a short, self-contained executable example that shows the problem you're facing?