Unless you have reason to split the first n-1 pieces as well, you only need the last one separated.

Once you have it, you replace the commata with quote, newline, appropriate number of spaces, quote

Voila!

while(<DATA>) {
  chomp;
  my ($first, $last ) = /(.+",)(.+)/;
  print $first;
  $first = " " x length( $first );
  $last =~ s/,/"\n$first"/g;
  print "$last\n";
}

__DATA__
"A","B","C","D"
"A","B","C","D,E,F"
"A","B","C","D"
"A","B","C","D,R,T"
[download]