Thats the saving grace for having to unseat Balgruuf. His monster kids no longer infest Dragonsreach.
Actually they are still there, in the basemant of Dragonsreach. And they still make snide remarks like "Great, another lackey here to lick my father's boots." and "Where can I find a good sweetroll in this skeever hole of a city."
I had trouble completing Mephala's quest which I started right after conquering Whiterun for the Stormcloaks. I could talk with the children, but you have to speak with the Jarl first and he had previously told me he needed a few hours to collect his things before departing Dragonsreach.
I think there would have been a way to move it forward if I had known the ex-Jarl had relocated to Solitude, but I ended up reloading my save just prior to conquering Whiterun.