Well, in my opinion, the easiest and safest solution is a mix of maclema and Borek answer:
Obfuscating code can be a big headach if you did not include it in your process from the start and if your aplplication is quite big: it's likely that obfuscation make your application corrupted if you used remote packages (and did not declare this to the obfuscator) if you used to many unTyped variables in Objects or dynamic classes ....
So: if you do maclema's solution on your big application and use obfuscation on your wrapper (which is a small app likely to be very easy to obfuscate) you're code will be the safest and the hasle the least.
Only a very angry pirate would take the time to reverse engineer the obfuscation to then decrypt the package .... Well if someone wants your application code soo bad it's either CIA related or you're already very rich (or both)
thank you all for your answers