More to the point as far as the Phylocode is concerned, Ceratopsidae is named after Ceratops while Dinosauria is not named after a genus (the existence of a Dinosaurus is coincidental). Article 11.10 of the PhyloCode requires taxa named after a taxon they contain to use the eponymous taxon as a specifier.
The way I see it, for the time being, there's no real value in changing the current situation, where Ceratops is the type genus of Ceratopsidae and Troodon is the type genus of Troodontidae. Everyone agrees Ceratops and Troodon are a ceratopsid and a troodontid respectively, so the names do the job of a type genus just fine. Ultimately the point of a nomenclatural code like the PhyloCode or ICZN is to resolve disputes over the use of taxonomic names, and I don't see any evidence that there's a dispute over the use of either at the moment.