ergh, I missed answering this part. Sorry, mate:
Players who have played long playthroughs, how did you deal with the food shortages? did it cause rebellions? did it cause "desertions"?
Castles and towns are different problems. Towns starve, Loyalty craters, Garrison drops (although only wounded, as of e1.7.x versions?) and yes you'll get revolts as soon as Loyalty is below 25 and Militia can beat the Garrison. But Towns can be, carefully, restored to Food Positive by external means. While you drive Prosperity back down to a manageable level, you can feed the town market. Generally, drops of around +200 Grain, +30 Meat +40 Fish +20 Butter +20 Cheese (if Prosperity above 4k; less below that) +10 Beer will get you most of the positives when they are counted (takes a couple of days) and you'll need to do such drops every 2-5 days while restoring the Town. Keep the Town's Village Market Parties safe and getting to/from town. Keep your vill's unraided if you can, heh. Long term, make sure the Garden is max level. But you know those last items. And eventually your Food Positive will begin to refill the Granary... and as soon as it starts that, all your Properity Plus modifiers turn back on, so watch out for Prosperity rise while you are still struggling to find sustainable levels.
Castles... currently can not revolt. They do lose all recruiting slots in their villages from low Loyalty situations. But so long as Prosperity + Garrison minuses overwhelm your direct Food Positives (internal, garden, village Hearth levels giving nil-6-12-18 ) you can not maintain or manually fill the Granary. Your garrison will drop as above. There is nothing to do except wait for Prosperity to come back down (and encourage that with Policies as said above) and you may be defending the place with your war party rather than a garrison in case of war.