The whole reference thing is a red heiring. Your question (as I understand it) pretty much boils down to "How do I split a list into pairs?"

my @vals = map { @$_ } @{ $hash{$key} };

my @pairs;
while (@vals) {
   push @pairs, [ splice(@vals, 0, 2) ];
}

$hash{$key} = \@pairs;
[download]