tl;dr– You can make safe spaces and defensive locations for your kitties. These can provide safety for the kitties as they try to eat or sleep, plus they can help deter bullying by making it a more difficult, less effective social strategy.
Make safe spaces for the littler kitty.
I'd try making safe spaces for the littler kitty. It wouldn't be a full solution, but at least she could sleep and eat without fear of being attacked.
The easy solution would seem to be getting large, clear plastic storage bins. Cut at least 2 doors into each, where the doors aren't large enough for the bigger kitty to get in. Then you can put different items in them: a food bowl, a water bowl, a bed, etc.. Ideally, your little kitty could then retreat to these at any time, eating/drinking/resting in peace without fear of attack.
Abrasive-cutting tools (like a Dremel) seem to work well for cutting holes in plastic storage bins, but there're other ways to do it too. I sometimes line the cut edges to help smoothen them out. A lighter might be able to melt the edges to be smoother, too, but haven't explored that possibility yet.
If your littlest kitty grows, you may need to cut the doors slightly larger. If the littlest kitty gets to be about the same size, then these small-kitties-only zones may not work.
Make defensive locations for kitties.
Some cats seem to like high, small perches where they can just barely fit. These are great defensive locations: a kitty can sleep there with relative comfort.
The trick's in it being hard for another kitty to get to the same location once it's already occupied. For example, if the location's accessed by jumping, but there's not a firm place for a second kitty to land, then it'd be hard for a second kitty to get a decisive win on the current occupant.
Discussion: Creating an environment that reinforces positive behavior.
An open environment where the largest kitty can attack any other might allow for bullying/controlling behavior.
An environment where kitties have safe places and single-occupancy hideouts makes it harder for kitties to bully each other. While they might still try to do so in public spaces, the effectiveness of their bullying is limited when other kitties always have a safe way out, especially when the bully can't prevent others from resting/eating in peace.