I guess it was either this ending or the one we got, it would have been a bit messy and confusing to have both. Personally I'm happy with what we got and this is just a nice little coda which I will personally take as canon.
Yeah I agree, whatever you think about it, this really was Amy's story with Rory, rather than Amy and Rory's story, it's always played that way throughout, even when Rory became a full time companion, with that in mind I think the actual ending we got was lovely, and I don't see how you could have had both.
At the end of the day you don't need to see something to asume it happened. Of course Amy and Rory would find some way to let Brian know, or the Doctor will; and, you know, they have other family too, how will they feel? At least Brian has an inkling what might have happened to them. We feel for Brian because we've met him, but Rory has a mum too, amy has a mum and dad etc.
As interesting as it has been, at times, to see the impact on family members of a companion travelling with the Doctor I really hope they knock it on the head for a while now.