One thing I really like about the depiction of the Kaylon is that, as far as I remember, nobody ever suggests that they were wrong to kill their builders, only to generalize their hatred of those builders to all organics.
As early as episode 3 they were trying to do serious storylines, and as early as episode 4 they were succeeding. I think it was always intended to be real Trek with the serial numbers filed off but sold to Fox and consequently advertised as a parody.