Symfony2 download page still says:
Be warned that Symfony 2.0 is not stable; use it with caution (current version of Beta 1).
So, I would just wait, but for Symfony2.
I'm not sure what you mean by source code protection, but it doesn't make sense to encode any part of either of the two frameworks, as they are both open source (and you have to make sure their licenses really allow that!).
Zend Framework 2 is still in the oven and, in appearance, Symfony2 will not be in beta until ZF2. If you can't wait, use the one you like best. Otherwise, wait for Symfony2 to exit beta, and then wait a little longer until it is smoothed.
Now about how to link the framework in your application, you probably need to write an installer. First, you can watch the symfony sandbox version to see how they did it. This is basically the unzip-it-and-it-works program. No need to install anything. This may give you some pointers.
Whatever you do, you need to write minimal script specifications that users can download and run to check if their system has everything your application is ready to run (check configs, php modules, etc. etc. ) For an example of such scripts, see SlideShowPro Director.
Subjective answer: I will go with ZF because this is what I know better, but having said that, the performance is wise, I had better results with Symfony. Obviously, ZF2 will see huge speed improvements.