If the runners are willing to allow someone close to be eaten by ghouls, rather than doing the run, then this is probably the wrong hook for the table. Perhaps because it feels too much like player strong-arming?
If so, then it can be removed a place, so that instead of the runners having someone close kidnapped, then a valued contact has had a loved one kidnapped, the Johnson knowing that the valued contact would come to the runners for help, and do the run on the contact's behalf (for a huge favour and a suitable payday). Of course, the runners could refuse but would lose a contact.
Also bear in mind that the Johnson is backed by a powerful group. Whacking the leader of the Ancients would certainly have repercussions... I don't think I would penalise reputation from the runners if they killed this Johnson, as he doesn't really deserve the title, and the rest of the shadowrun community would probably chink glasses for removing him for his outrageous behaviour. But I think it's important to realise that the reason that the Johnson has done this is not because he's an asshole, but because he is a very desperate person, who has lost a child, and wants them back. Having him break down in tears in front of the runners could make them realise just how wounded he is, and maybe open the door to negotiations...
It's an important point that the child may never have been taken by Urubia in the first place, the Johnson is simply jumping to a conclusion. Imagine the child turning up the day after the runners have whacked the Johnson, none the wiser of the trouble they have caused.
If the runners need an "in" to carry out the run against the dragon, then the dragon may have taken a "voice" who, although they fully back their master in their schemes, is privately against the kidnapping of the children, and has reached out to the Johnson, and is willing to provide information to assist in the investigations. The runners may only initially find out that someone at the other end of a commlink has info for them, but nothing else.
I hope this gives a few ideas of how such a campaign could be handled. YMMV.