XEP-0060 is supported by Prosody since a long time ago, as a component. I think you just need to enable it. See https://prosody.im/doc/pubsub, you need yet another extra subdomain and should include it to your server certificate.
Okay, I see the issue. The problem here is PubSub component in Prosody doesn't support Section 7.1.5 (a.k.a. publish-options) of XEP-0060, which affects the usability of OMEMO. Anyone has the plan to implement it?