Fear of the unknown is a normal part of life for all of us. Children and adults alike.
I would try to remain positive and firm that everything will be Ok for Eliza. Once she starts school I bet she will feel more comfortable without her sister around than she imagines.
I think you are right on about keeping their playdates and sleep overs separate. Especially regarding what happenned last time.
It also sounds like she is picking up the "Emma needs extra help" vibe and wants to find a way to show you she might want a little "extra help" too.
I am sure you are finding ways to show her that she is special as well. But as the focus is on her sister right now, even if you make an effort to show she is special too, she will still pick up on it. So dont think that this is some serious sign that she is missing out on love etc. . . It sounds like normal behavior under the circumstances.
I know this is a big decision for you and you are concerned how it will effect both of your daughters. But from what you say they are already used to being in different classrooms. The overall difference will probably be pretty pretty minor when it comes to day to day life. They just dont know what to expect.
IT sounds to me like you are really doing a wonderful job and I have confidence that things will turn out well after a very short period of adjustment.