It sounds like you have been handling it well, helping her understand how her little brother feels when she is short with him. I agree with Clarity's suggestions also.
I have an almost 9 yo stepdaughter, also here with us for the summer (along with her 5 yo sister) - and their dad and I have a 2.5 year old, so I can relate to the challenges!
Our 9 yo is certainly more 'modest' than she used to be in the past - I think it's natural to want to put up those physical boundaries around that age, and it takes a bit of getting used to when as a parent you're used to everyone trooping around in the buff (which used to be our MO when she was younger). I agree with reassuring her that adults and older children have different privacy standards than little kids, so she doesn't feel like her own clothed state is threatened.
Does she have any other younger siblings? It may be a big shift for her to have to deal with a little one during the summer, and she may simply not have a sense of what is age-appropriate. When my 5 yo stepdaughter complains about her 2.5 yo half-sister's behaviour (lifting her dress, shouting 'mine!'), we talk about how her little sister is right on track for what 2.5 year olds should be doing, and how she did the same things at that age. Maybe your stepdaughter's dad can chat with her about what she was like at 2.5, reminisce with her a little?
You can also both tell her how her little brother looks up to her and values her as a big sister and role model, and encourage her to take that seriously. Don't forget to praise her when she is gentle and helpful with him! Positive reinforcement will help. Our 9 yo stepdaugher is usually pretty patient with the 2.5 yo (it's the 5 yo she can't stand!), but once when she was mean to her, I pointed out that 'she is crying because she is so surprised and hurt that you would use that voice with her. She is too little to understand why you are mad, she just knows how that voice makes her feel. She really loves you a lot and didn't expect you to speak to her that way.' She felt pretty bad, and adjusted her behaviour accordingly.