I have looked at software protection in general for my own projects and the general philosophy is that complete protection is impossible. The only thing that you can hope to achieve is to add protection to a level that would cost your customer more to bypass than it would to purchase another license.
With that said I was just checking google for python obsfucation and not turning up a lot of anything. In a .Net solution, obsfucation would be a first approach to your problem on a windows platform, but I am not sure if anyone has solutions on Linux that work with Mono.
The next thing would be to write your code in a compiled language, or if you really want to go all the way, then in assembler. A stripped out executable would be a lot harder to decompile than an interpreted language.
It all comes down to tradeoffs. On one end you have ease of software development in python, in which it is also very hard to hide secrets. On the other end you have software written in assembler which is much harder to write, but is much easier to hide secrets.
Your boss has to choose a point somewhere along that continuum that supports his requirements. And then he has to give you the tools and time so you can build what he wants. However my bet is that he will object to real development costs versus potential monetary losses.
