Firstly, you should consider that you're fighting an uphill battle—if your app is popular enough, the other guys are probably able to patch your app to remove any checks you may perform.
If you do decide it's worth the effort, the first place to start is Apple's guidelines for alerts.
As with any other error message, you should include three things:
- A very short error title, phrased in the imperative (users should be able to read this quickly without thinking too hard)
- A (slightly) longer error description with justification of the behaviour (this is useful for users to Google the problem)
- A clear call to action for the user (what the user can do next)
In this case, the seemingly appropriate behaviour according to Apple's guidelines is:
Your phone appears to be jailbroken, and so for security reasons [App Name] cannot be loaded.
[More Info] [Quit]
That having been said, Apple explicitly says you should not quit your app programmatically. Since your app is apparently non-functional on jailbroken devices, I'm not sure what alternative you have to a Quit button. Perhaps a deliberately non-functional version of your app's starting screen (in which case the button just becomes OK).
In my example, the More Info button would take the user to Safari with details of your justification, and—importantly—instructions for how the user can report a false positive to you.
For completeness, here are some other examples of a similar message from other apps (including one from Apple's iBooks):
And here's a pretty familiar one from Microsoft that is deliberately worded to avoid being too accusatory toward the user: