There are several things to notice here; one is the consideration of actually telling one that an e-mail address is already taken; as this helps both hackers and decreases privacy. An example for the latter is, say that one of my friends has registered on a NSFW-site, I could just check which one of my friends are on it,...and blackmail them! Something to think about.
Now, to try and answer your question, I'll start with a question: Why are people having a difficulty to actually differentiate between the register and login phase of your website? Perhaps some things are, in fact, unclear. You could, for instance, stop the auto-pilot, by asking the user to confirm their password once more.
Another way is to accomodate as much as possible, by simply allowing the use of SSO (Single Sign-On) options like logging in with facebook, twitter, ...