No, I agree. If the word is written one way, it should not be pronounced differently. There are beginners on this site who don't know conjugations, and it's very misleading/discouraging to not be sure what to learn.
Along those lines, it would be super great if the verbs were presented all in dictionary form, since that is the basis for any conjugations. I've run across a few already put into て form, which makes them not even look like verbs to beginners. I'd also love to see the English translations for all verbs follow a standard "to ~~" kind of pattern, so you don't see something like "walk" and wonder if it means "to walk" (verb) or "a walk" (noun).
The thing that bothers me even more though is when some of the vocabulary words are written in kanji with furigana above them, but the furigana reading doesn't match the roumaji reading. Almost always, the furigana is wrong. I'm not sure why that is, but I really hope it gets fixed soon. I've had to use Rikaichan to double-check many words.
All in all, this is a wonderful site, and a great resource. I wish there were a better way to suggest improvements though, or even for more advanced users to help edit things. With even minor improvements, I think this site could be even more beginner-friendly, since we've all been there! : )