User blog comment:FairyRaven/Fairy Tail Chapter 387: Tartarus Arc, Part 4: Father and Son, Review and Commentary/@comment-24467372-20140606101911/@comment-7418318-20140606105104

I agree with B214. Even if the branches couldn't keep functioning (which may or may not be the case), they people there would at least still be alive.

With the other top-brass gone, Doranbolt is probably the highest ranking member of the Magic Council and thus has the authority over the surviving branches, including their fighting forces.

And I don't see why the Rune Knights would suddenly refuse to follow the orders of their superior just because his superiors are dead. Sure some or maybe even many might have deserted, but surely not all.