Pinning the intermediate CA should work. Alternatively, calculate the cost of updating the cert pinning mechanism if it's custom and compare it to paid, 1 year certificates (though those will go away eventually too).

On the other hand, if you're using an app specific server, there's no need for you to use public certificates. A self-generated one with a five or ten year validity will pin just as nicely. That breaks if you need web browsers or third parties to talk to the same API, of course.