Well, I'm glad that I'm not alone in thinking it makes some sense. I agree it would be a REALLY lame thing for Kishi to pull on us. I'm sick to death of the "bad guy was really good at heart" routine as well. There IS evil in the world, and taking that element out of the series kinda...ruins it.
As for Madara trying to kill the current Kages, well I have two thoughts on that. One, they represent the old system and old grudges (even though they work together now, I don't know that they'd willingly give up their villages after the war.) and even if that in itself isn't a factor, well, Madara Obviously isn't above sacrificing others (or twisting their minds like with Obito)for his goals and the greater good as he sees it.
All of the other ninjas that have died could feed into the whole pain of loss theme that the manga has gone on about again and again. Their deaths at Madaras hands help give the rest a shared painful event to help them rally together. An easy victory wouldn't force them to work together like a real deadly conflict.
Hell, it even worked on Sasuke.