Agreed on most counts, though it's likely that there is a little validity in those 'real' excuses as well. Just not nearly enough to fuck with Gensokyo and history so much, especially when there are alternatives (and/or if Sanae had been allowed one jet flight before the end, but them's the breaks). How did they pull it off, anyway?
I wonder... changing the history of someone is more trouble than it's worth, but wasn't there some earlier speculation about making someone not a youkai? If there were a way to end it or hide it without messing with time, then that might work better. It's the how that's the problem, and I don't have any clever ideas for how to do that... I'm not sure if Purvis' Yukari would be able to, and I can't think of any other usable routes offhand...