An upfront warning: only an Apple representative can give you a definite answer to whether or not something will be acceptable on the App Store, so to be certain you'll want to check with them on this. The most the rest of us can do is speculate.
PythonKit uses publicly available capabilities and interfaces, so I don't believe the normal precautions about private API usage or undocumented features apply.
As a result, I think the remaining concern is about section 2.5.2 in the App Store Review Guidelines
"2.5.2 Apps should be self-contained in their bundles, and may not read or write data outside the designated container area, nor may they download, install, or execute code which introduces or changes features or functionality of the app, including other apps. Educational apps designed to teach, develop, or allow students to test executable code may, in limited circumstances, download code provided that such code is not used for other purposes. Such apps must make the source code provided by the Application completely viewable and editable by the user."
If the Python code is self-contained within your app bundle, it sounds like you'd be fine under the above restriction. Also, before deploying an application that uses PythonKit, I'd make sure it can handle the variety of Python installations you'll find on your users' machines (different Python versions, missing Python, etc.) because I know that can be a challenge.