This. Absolutely this!
I'm of the opinion that there's no wrong way to split trip costs as long as it's negotiated clearly and everyone agrees on the outcome. On the majority of trips I've shared with friends, we've split everything equally by person (so when my housemate and I traveled with two married friends, each person paid a quarter share regardless of relationship status). The last time I went to WDW with my mom, though, we went halvsies on the resort but then she paid for all the food because it was her decision to upgrade to a deluxe and incur the extra costs associated with it. I've arranged at least one trip where I offered to pay the full cost of the resort on the logic that it'd cost me the same whether I was solo or had someone in the room with me, and my companion just paid all their additional expenses beyond the room.
But all of those were pre-negotiated, and all of them were things that both/all parties were happy with. My starting baseline for those kind of financial negotiations is an assumption that every person who is going will be paying an equal share; anything different is an adjustment that must be agreed upon. So yeah, I'm with you on assuming that sister and boyfriend should expect to each pay 1/3 share since you had not offered to pay half. I get why she made the assumption on half an half (she'd be paying half if it were just her, and it doesn't actually cost extra to put him in the room--unless I've misunderstood how Disney charges), but it's not what I've ever assumed or had a friend assume on a shared trip. I don't think you're out of line at all.
I'm going to refrain from making assumptions about your relationship with the boyfriend or how you feel about him coming since you didn't really say. I'd just say that whatever your preferences are about him coming or not coming, about what share he has to pay, etc., you have to communicate it. I know if it were me I'd feel uncomfortable having to speak my preferences so directly, but it's better to deal with it now than spend the trip resenting either of them for having misread the situation.