It depends on how far the fake went. I have seen where the QB started to kneel and the refs blew the whistle thus ending play before the QB reversed his motion to make it a fake. So I wouldn't have him go that far. I'd just have the QB go to the line making that "we're going to kneel now" motion and have everybody line up for the kneel (which is a highly distinct formation), then have Ben stand up good and tall after the snap (the nice part about how big he is, if he stands up straight nobody will confuse that with an intent to kneel) and make the sneek dive. The action should happen fast enough that Indy won't have time to react but still be clear enough that the refs won't blow the call.
IIRC, the fake kneel is now illegal either in the NFL or college.
The only problem with that particular fake is that, when it's do-or-die, you're going to have somebody diving over the center trying to knock the ball loose. Heck, let's take a look at the Panthers/Bears game. The Bears did dive over the center, and the ball popped out, but the refs had already blown the whistle.