I think so, yes. You're definitely not supposed to have any hyphens breaking up words, for just that reason. I wasn't sure about 'punctuation' hyphens at the end of lines (I can't find any definite statement against them, but The Yellow Poppy doesn't have any, which would be unlikely to happen by chance), but, thinking about it, I reckon they would result in extra spaces being added when the text is rewrapped ('to- morrow'). So I'm going through and getting rid of them too—which means more line length woes :D

The ebook for TYP does have nice even margins, which is presumably down to something in the html—I'm sure I'll have to figure that out at some point...