I like Derby's idea. If I'm understanding it correctly, you dos2unix every script after it's uploaded, as needed. That is, all scripts on the server will always use standard unix line endings, period.
In addition, while you're at it, you could also even have your automated tool send an email to the guilty Windowsy uploader, courteously asking that they please either use text mode for scripts with their ftp client next time, or else to please manually convert line endings before uploading.
Though, I see that this doesn't answer to the Ovid's OP, since he was looking for something that "doesn't require manual intervention".