When the OS reports that the user is using a FAT partition, or when you detect that the user is probably using a FAT partition (maybe you can look at the few file times in the partition's root directory and check if they're all even numbers), and the user is not using --modify-window=1, please print a warning onscreen, warning the user to do so.
This will help newbies who didn't read the manpage. I originally didn't read it, and many of the people who come to irc.freenode.net haven't read it either.
I would be disinclined to add this to the main version of rsync. Rsync generally doesn't devote effort to second-guessing the user. Not reading the man page is not a supported use case.
I neglected to use --modify-window=1 when I first started using rsync. More importantly, think how other people have made the same mistake. Who knows how many hours, days, or weeks of unneeded syncing we (the group as a whole) have waited through in total until we've learned.
"With very few exceptions, users will not cuddle up with [a] manual and read it through before they begin to use [some] software. In general [...] users are trying to get something done, and they see reading the manual as a waste of time, or at the very least, as a distraction that keeps them from getting their task done." -- http://www.joelonsoftware.com/uibook/chapters/fog0000000062.html
There's no good way for rsync to know that it is copying onto a FAT filesystem.