Rather than doing all the substr's, couldn't you just do

$in = s/^\((.*)\)$/$1/;
my @splat = split(/,/, $in);
my ( $depth, $left );
while ( my $c = shift @splat ) {
     $left .= ( $left ? ',' : '' ) . $c;
     ++$depth if index($c, '(') >= $[;
     --$depth if index($c, ')') >= $[;
     last if $depth == 0;
}
my $right = join(',', @splat);
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and then recurse on $left and $right? (Maybe searching each time for the parentheses is as hard as substr'ing, though.)

UPDATE: Per BrowserUK's response, the answer seems to be “Yes, but why?” I always thought that substr's were very expensive, but apparently not. Hurrah for premature optimisation!