Maybe it was just a dharma drill that happens so often and automatically. I say automatically because if the people making the drop knew the dharma were dead then they would'nt.

According to the Sri Lanka video released as part of the Lost Experience, DHARMA sends regular medicine and food drops to the island. So,it was from DHARMA, whether they realise most of DHARMA is dead or not, is another question.

Maybe Mikhail kept the food coming by pretending to be Dharma, using The Flame - which would explain why food becomes short eventually at the barracks, after The Flame was destroyed. If you look carefully when Locke goes into Ben's kitchen in season 3, there's hardly anything in the fridge and Ben keeps the scraps of chicken even when there's hardly anything left. Which could also be the reason they moved out of the barracks to go to "the temple"... perhaps there is food there. After all, if they are running out of food, the last thing they would want is to kidnap all the Losties' women and children. I'm liking this theory.