According to the story, the guppies that changed somewhat were still of the guppy species, and did not mutate into some other species altogether. That may be evolution as you know it, but it does not prove the ToE in any way, shape or form.
I didn't make myself clear. The guppies actually speciated into two new species. They underwent reproductive isolation and, after a number of generations, were not able to breed. This defines speciation, because now, genetic information cannot be shared between the two populations, and evolution can only occur on the population level.
Suppose that instead of becoming smaller and changing mating habits, which are not small changes at all, one population was selected for larger fins, so they could swim faster to escape predators. Then suppose one population was selected for a longer jaw, to grab more food. After a number of these selection events, the two species would not look anything like each other, as different as tuna and swordfish. This would be evolution, and as always, people like you would contend that the two species never had a common ancestor.