With today’s announcement that Jonathan E. Johnson III has been appointed president of Overstock.com (NASDAQ:OSTK), it got me to thinking about the future of the company. I don’t think many people would argue with the suggestion that Patrick Byrne is one of the worst CEOs in the country. He has been for a while.

And I don’t think many would disagree that shareholder value is not enhanced when Byrne is busy running around commenting on message boards and blogs, evangelizing his naked short selling conspiracy theories, and being a “journalist” for his Deep Capture website. Really…. How focused can one be on running a company like Overstock.com with all these other “interests”? Even Byrne’s dad thinks he can’t do his job with all this nonsense.

How about the waste and misuse of Overstock.com’s corporate resources? We’re talking things like:

• Using the Overstock.com servers to host the Deep Capture website
• Diverting Overstock.com revenues to the Deep Capture cause via this message on the Deep Capture website: “Click here to shop Overstock.com. 5% of your purchase will go to support this effort.”
• All the time that the board and other executives must have to waste cleaning up after Patrick Byrne, fixing his messes, and generally dealing with fallout from his nuttiness.

I’d even go so far as to suggest that the shareholders of Overstock.com have been cheated for years. Not only do they get a horribly incompetent CEO, they get one who can’t be bothered to do his job. On the other hand, if shareholders haven’t figured this out by now, maybe they deserve whatever they get.

So with all this in mind, what happens if Patrick Byrne is planning on leaving Overstock.com (presumably to continue being a full-time message board troll and naked short selling evangelist) and Jonathan Johnson takes over running the company?

I think it’s safe to say that the company would be better off. I can’t imagine that anyone would believe that Overstock.com needs Patrick Byrne there, or honestly believes that he’s a good CEO. So his departure should likely be viewed as a very positive move for the company.

On the other hand, there’s a big risk if Patrick Byrne leaves. The company has been bleeding red ink since 2000, to the tune of almost $239 million. The company has never turned a profit in any year, and the two “profitable” quarters that Overstock.com has shown are questionable. What happens, though, if Byrne leaves and the company continues to lose money? Then what’s their excuse?

Right now, Patrick Byrne is obviously incompetent and a large part of the reason that the company has such awful performance. (I know, I know, Overstock.com supporters. The company is losing money at a slower rate than it used to. Big accomplishment!)

If Patrick Byrne leaves Overstock.com and the losses can’t be blamed on him, do we then have proof that Overstock.com is just a bad company in general?