How does protecting the source code of the program protect it from being copied? The protection comes through legal means like licenses and patents. Anyone that just wants the binaries, will just copy those. Anyone that wants the algorithm, can disassemble the machine code. Perl just makes it easier to figure what is going on. Anyone who isn't afraid of legal means won't be stopped by an obfuscator.

In some ways, Perl source could be better from a legal standpoint because it is explicitly available. The competitor who looks at your product has a harder time proving they didn't look at the source code because it was sitting right there on their hard drive. With a binary C program, they can claim legitimate reverse engineering. It is also likely that their source will be written new using the algorithm and concepts. With Perl, they are more likely to get caught copying the source directly and producing a derived work. Then your attack laways take them to court and win the big bucks.