Honestly, I am not sure about anything related to this law. I am also not UK-based so I don't know haw exactly is the EU directive implemented in UK.
I live in the Czech Republic and here you can become so called "person identified for VAT" which (if I understand correctly - IANAL) enables you to use mini one stop shop for selling over the border while internally (selling inside the country) you remain in non-VAT regime.
Our law is based on the same EU directive as yours so I suggest you check whether your law also offers something like that.
It is still more complicated than it should be (I think the whole concept of VAT is bad) but I hope it is not as bad as registering in all EU countries.
I will also consider 3rd party services like http://www.taxamo.com - I am not related to them, I am just sharing that because you might find it useful.