If they truly pull this off we should all be advocating apps like DeltaChat (f-droid.org/en/packages/com.b4…), an E2E encrypted chat app that utilizes GPG encrypted emails in a user-friendly fashion.
And best of all the whole "walled garden messaging service" deal would be a thing of the past - all a participant ever needs is ANY single email provider and the DeltaChat app.

Wonder how they'll try to ruin a decades old backbone internet service like the MTA protocol?

Truthfully?!
In this case the whole act appears toothless to me - any terrorist or child abuse organisation may have a tech savy person among their ranks that can utilize open source software in a malicious way.
I was under the impression that the EU strives to install software backdoors or scanning engines in any messaging protocol. This sounds more like an attempt to get access to big data at large under the guise of protecting the innocent - far from purposeful.

In any case, thank you for the clarification, in a nutshell it may be simply up to us tech savy people to advocate for using federated and self-hosted services again. In a way this would return the internet to a more community/people driven way of operating - and I am all for that, personally!