There's really no way of hiding Python source code and prevent the users from being able to know what you do to their systems. However, that does not mean that the program has to be Open Source. That depends on the license and you can use which license you want. Being able to read the source code does not mean that the user is allowed to edit it, or redistribute it. That's up to you. This is true for all high-level languages. Web applications, for instance, always have their source code visible to the user. That doesn't mean you are allowed to use it in other projects without the developers permission.
You might want to have a look at the Geanie language. It is a new language that has features similar to Java/C#, but with a syntax that resembles Python. Genie compiles to C, which means it's platform independent, but also that it is extremely fast. And C, of course, compiles to native code.
Unfortunately, Quickly doesn't have templates for Genie yet.