This is a shell problem, not a Perl issue. cmd.exe uses double quotes as string delimiters. You can avoid this with Perl by using other Quote and Quote like Operators. For example, this will likely work (assuming there are no other issues with your command):

perl -ne "chomp; print qq{$_\tO\n}" jane-austen-emma-ch1.tok > jane-austen-emma-ch1.tsv