I would say that you should code the required logic in XS and only provide binaries for those modules that are under NDA. It means some of your code will be restricted to the platforms you support but I think its really the only way you are going to keep the code secret. (Well, they can decompile the libraries but...) Incidentally doing "perl" in XS/Inline::C isn't that difficult, and can offer some nice speed improvements.
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