I was thinking about this and it seems like if you really wanted to secure your application from hackers there is really only 1 way to do it. You can implement all kinds of fancy methods of insuring your application is licensed and paid for as described in the google article but all it takes is a good hacker to decompile your application and find where the code is and then comment it out or change a function to always return true.
Instead, implement some portion of your application that is required for use in jni/ndk, and check for validation in that code. It doesn't have to be extremely complicated code but you can't just put something like a function (eg. checkValidity) as a user could easily comment the java call that calls into the ndk. Instead you should make some call to your ndk to actually do something that is non-trivial for your application to run -- something the user can't just comment out or switch out with a defined function that does the same thing. From within the ndk code do the verification of your application's integrity/licensing and if it fails kill the application or whatever you need to do.
In order to bypass this the hacker would need to re-implement the ndk code or reverse engineer it.. Which should be much more complicated and not worth while.
This obviously isn't a simple solution and still won't guarantee your application never gets hacked, but it should be much harder to break than the other methods..