If your string result is so huge that the copy really is a problem, you can temporarily make an alias like this:

for my $seq ($_[0]->seq()) {
   # in case you need to reset the first match position
   # (avoid pos() on huge strings)
   # $seq =~ /\za/g; 
   $CG++ while $seq =~ /CG/g;
}
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update

Interesting enough, due to the way the perl internals work, this doesn't save you memory compared to

my $seq = $_[0]->seq();
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during the processing, but the gain is less wasted memory when $seq goes out of scope again (this isn't a memory leak, perl will reuse that memory if the scope is entered again)