Why does this stop you from pinning your certificate?

You only care about pinning when you fear that a third actor somewhere between your server and the end client might MitM the connection with a valid certificate.

If a third party controls your keys, certificate pinning is useless to prevent against attacks from that third party or governmental agencies.

Most HPKP deployments pin to root or intermediate certificates of CAs (usually 2 separate CA entities, in case something happens to the primary CA) - meaning in a typical scenario, the attack surface is approximately the same.

Not sure if this approach is common in native applications that pin to keys as well.

Obviously. That doesn't mean pinning is impossible or useless against other threats though, so I don't think the argument makes sense in that general way. I bet there are tons of apps running/with backends running on AWS that should have certificate pinning.

It's always possible to get the public key, e.g. see the accepted answer here:

http://security.stackexchange.com/questions/16085/how-to-get...