This sea slug is (according to journalists, a huge qualification) part animal and part plant (link). Thus, the slug defies conventional clades. It does not fit into the evolutionary tree. Will any atheists accept this evidence and discard evolution? Probably not. Most will simply try to build a new tree and assume that one can be built until they succeed.
Incidentally, I suspect that this sea slug will turn out to have a parasitic plant living symbiotically with it, or something like that. If so, it will fall more or less neatly into the existing clades.
The explanation in the article is that by an unexplained mechanism (it sounds so much nicer than "magically") the slugs steal genes from their food and pass those genes on to their offspring. If this is correct, then the slugs fit in the slug clade and simply have a very unusual distinctive trait of being able to steal genetic code from other organisms.
Of course, by the way, the ability to steal genetic code from other organisms is a great deus ex machina to avoid letting the clading system be falsified by the evidence of nature (much like the deus ex machina of parallel evolution).