I think I'm understanding your problem. The "characters to be updated" section can be described simply as "characters in this guild snap shot that are also already on your site". They are being updated even if nothing is really changing, but it's important to show everyone in the upload.
Since all the other sections check the rosters and says "Oh, these guys are new" and "These guys aren't in here" and "These guys have a different rank", why can't we have it remove people who aren't changed?
I realize the load would take slightly longer, but it would make this less of a bear for others in my guild to manage?
Also, it would kick ass if when you did a GRSS upload for a raid, it would ask at the end "Do you want to update your roster?" and just jump to that too.