I've finally had an opportunity to spend some time analyzing the problem you had loading that large SVG.
Your file did eventually load, although I think it may have taken as much as half an hour to do so on my machine.
In Inkscape, sibling XML nodes are currently kept in singly-linked lists, which are not an efficient data structure when dealing with large numbers of siblings (in this case, more than 87000).
It is possible to use faster data structures, but they would come at the cost of using extra memory. As it was, once the document loaded my machine ran out of memory when the renderer kicked in.
So, I'm not really sure what the best course of action would be. I do think we have a problem dealing with large documents in general.
I am CCing the development list for their suggestions.
-mental