My main tree is with Family Tree Maker on my computer. I put everything in there. But when I uploaded that tree to Ancestry and when I add things to the Ancestry tree, I put "living" as the name of living people and don't connect records to them, etc.
Your sister doesn't have to have a reason not to want her name and info on an online tree. I feel you should respect her wishes. And if she doesn't want her info there, you can assume it also applies to her children (unless they are grown and give permission).
I suggest that you don't make Ancestry.com the keeper of your only tree. Do one on your computer too. And put ALL the info there.