The only thing I can think of right now is to have the index.html auto-forward (with like Flash or whatever you like) to the 'home' directory. So truely your root directory is still
www.mysite.com , but anything asking for this root folder,
www.mysite.com , or
www.mysite.com.index.html will get forwarded to
www.mysite.com/home , and you can put other pages in the root that will not do this, as well as folders and files that behave like normal.
I dunno though, I think there is another better way. I know when you tell PHP, for example, to write to a file in say
www.mysite.com/orders , you would write the link from
www.mysite.com/home as '<a href="../orders/orders.txt">, and even if the root was
www.mysite.com/home (literally in Apache code as C:\apache\htdocs\home or whatever, as you know), PHP would still go up whatever level you want in the OS and back down to the folder 'orders', in this case. Without any regard to permissions.
Correct me if I am wrong! But as I have found this to be true, then there must be a work around. As you know, this method of linking in PHP doesn't work in regular HTML; you could write a link "../../../../../../" ../ forever in HTML, and you would still only end up in the root folder. But in PHP it does matter, you can end up anywhere.
Alright, just ranting and thinking. I will keep think about it, hope there is a solution for you!