this looks like a major disadvantage to me.
email replies was a great feature!
the drawbacks that you mention are not that big.
people are self-centered, and want to know immediatly when somebody replies to a post they have made!
the problem with the newbie users can easily be solved by just adding some information in the email, telling newbies not to reply via email (newbies as newbies read such stuff).
although replying via email would really be some kind of killerfeature!
so I am asking desperatly to re-introduce the reply-to-my-post one way or the other!!
(current version: 6.3.2.)
ps: please excuse my long location-entry