I think the whole Debbie Cook trial is giving credence to the idea that the problem with Scientology is the current regime. (I find myself feeling sympathetic for Debbie Cook, despite knowing better.) Regardless, Scientology's overall situation will never change.
I think it's unlikely that the Church will emerge with a third leader. Unless DM decides to off himself - which I suppose isn't beyond the realm of possibility - he is unlikely to give up control of the Church for the greatest good (which is off-policy). That said, with all its assets, I don't see how the Church could possibly go out of business. Although the focus on DM could have one positive effect: Investigation leading to elimination of the Church's tax-exempt status.
I suppose it's possible that a re-formed Church will arise with Marty Rathbun or someone similar at its head.
Regardless, Scientology will end up back in the news, because the abuses are hard-coded into the tech. We seem to forget that there were no "good old days" of Scientology. Read The Scandal of Scientology (
http://www.xenu.net/archive/books/tsos/sos.html) or listen to David Mayo's lectures (
http://www.freezoneearth.org/downloads/files.html - scroll down) for a reminder that everything happening now, has happened before.
Scientology is a scam, and no amount of PR can change that.