What I take from Joao's theory, is not so much challenging Guth and inflation, as to point out that we, or rather the physicists involved in these theories/discussions, were taking the speed of light being a constant factor, as a given. Guth presents strong arguments, but, as with almost every new theory, his has some "shortcomings". Guth relies on dark energy to account for some of the expansion of the universe. In addition, his theory for the beginning of the universe we know - quantum tunneling and parent universes - just dont seem to fit with what we "know", as of now. However, I am a believer in the "multi-verse" concept, which Guth's theory backs up quite well.
Joao's theory, being much more controversial and "out there", is also slightly more reasonable - in my eyes - in its assertion that the speed of light, which we know varies according to the medium through which the photons are traveling, may also vary when traveling through a vacuum. This too, along with Guth's theory, would call for the rewriting of our entire understanding of the universe, down to what I believe is the prettiest equation in physics; E=MC^2. While devastating to known physics, I think the confirmation (I realize that inflation has been "confirmed", but that was using other known forces, such as dark energy - as stated above) of one or the other would be the biggest step forward to our understanding of the nature of the universe, as well as our place in it.