I think you need to close the loop on this malformed feeds.

First, in preferences you should be able to say as a user if you will accept bad feeds. If you don't want them, then the old pop-up works fine. If you are willing to accept bad feeds, the the approach on a single pop up when subscribing is fine.

The reason I like this approach is that the author will know that they will lose some number of subscribers if their feeds are bad. This add incentive to make good feeds.

Second, to completely close the loop, the author needs to know. I suggest including the author's email address in the pop up so as a user I can immediately let the author know that I don't appreciate bad feeds. This will be real incentive.