They died because they were genetically related, and were thus similarly susceptible to the same microorganisms. The killer is no longer recognizable, having mutated long, long ago into another path altogether. It would be sheer speculation as to what the intelligent species on Earth would have been, had this not occurred. However, most habitable planets do indeed evolve reptilian species, not mammalian, as the dominant species. This is simply first come, first serve.
Reptiles evolve long before mammals, and have a head start.
It does not follow, however, that the intelligent species is mammalian only where the evolving reptilian species has had a catastrophe. Most planets evolving mammals as the dominant intelligent species have not had such a history. Many factors come into play, among them how difficult life is for the various species. A difficult life, while a curse at the moment, induces intelligence.