Reading the executive summary of the EU report you find that this is indeed the vision of the authors (ConsenSys AG). I tend to disagree and I give you my reasons:
The authors report that public chains are not ready for scalability, interoperability and sustainability. I happen to operate in environment where these issues are all addressed.
On the other hand permissioned blockchains are hardly ever to be considered blockchains. It is way more difficult and expensive to get a permissioned blockchain to have all the characteristics (and benefits) of a public blockchain.
It’s much more easy to better scope your project and use the proven public infrastructure instead.
I do agree with the authors that focussed blockchains will take off first, but not in the form of permissioned chains. Rather as public sidechains in an interoperable multichain environment.