My husband and I are both certified teachers who have experience in both charter and public schools. Unfortunately it is not just a choice between charter vs. public school. Each charter school is different - based on who sponsors the school (business, university, school district, etc), who teaches there, what curriculum they follow, how long they have been around, etc. If you really want to choose the best school for your children, you have to visit each school, ask questions, and talk to other parents.
Not all public school teach reading by sight words and not all charter schools teach reading phonetically. The same goes for the curriculum at the school. Sometimes the teacher or the administration has a big say in the layout of the curriculum, but that depends on who "sponsors" or runs the school. The larger charter schools, run by a university or a business, often have a set curriculum (sometimes very rigid) that cannot be altered.
The size of the schools you consider will determine whether there are options for your girls to be in separate classes or if they will have to be together. Some charter schools are quite small and only have one K classroom and one 1st grade classroom, etc.
I am not sure I really have advice about keeping the girls together or not. I don't have older kids and haven't been through that yet. If it is a small school, they may see each other quite a bit even if they are in different classrooms. That could be one of your questions when looking into schools - do the classrooms interact and share lessons or activities ever? Would they have recess or snack together? If it is full day K, would they have lunch together?
Have you asked the girls what they would like? They might be able to tell you their preference.
Good luck! Choosing a school is not an easy or quick task most times, but hopefully you will be happy with your choice and won't have to do it again later! :o)