1) Wilhelm His is not necessarily a reliable source of information regarding the scientific status of Haeckel's work. He and Haeckel were openly hostile to each other his opinion could hardly be considered unbiased. And some have questioned the accuracy of His's drawings as well.
2) There is no historical documentation for Haeckel having ever been tried much less convicted of fraud. This story appears to be a myth.
3) While it is technically correct that humans and other terrestrial vertebrates do not posses "gills" as embryos, they do posses structures that appear to be homologous in great detail to the structures of fish embryos that develop into gills. The recognition of this fact is not dependant on the acceptance of evolution. However the retention of these gill-like structures in the embryological development of terrestrial vertebrates is best explained by descent with modification from a fish-like ancestor.
4) The evidence from embryology (such as the existence of pharyngeal pouches) is not in any way dependant on Ernst Haeckel or his drawings, fraudulent or not. Or as Michael Richardson put it:
On a fundamental level, Haeckel was correct: All vertebrates develop a similar body plan (consisting of notochord, body segments, pharyngeal pouches, and so forth). This shared developmental program reflects shared evolutionary history... Haeckel's inaccuracies damage his credibility, but they do not invalidate the mass of published evidence for Darwinian evolution. (Richardson et al. 1998, p. 983-984)