Well the CAE (and with that the MV scheme for sheep) hasn't got anything to do with limiting the gene pool, if everybody would do it. Unlike scrapie, where the a large number of breeding males in particular were excluded because of their genotype, CAE and MV are (as far as I know) not linked to genotype, but are acquired viruses.
So really the problem is that it is not a compulsory scheme for every goat/sheep breeder and therefore only limits the gene pool because not all of us can justify the (initial) extra expense of joining. And because it makes life difficult if you show your stock, it is again not something most of us want to do. And the reason it is not compulsory is that there is (to date) no proven link to human disease (either via milk or meat consumption).
But the commercial sheep sector I think is now moving ever more to MV accredited status, if you look at the number of tups for sale for example.