It's been a weird summer for Whole Foods Market (NASDAQ:WFMI), Wild Oats (NASDAQ:OATS), and their shareholders, considering the Federal Trade Commission's efforts to block their $565 million acquisition plan. Now there's been a victory for the companies: A federal judge, Paul L. Friedman, denied the FTC's request to block the deal.

It's nice not to feel as though we're living in bizarro world for a change, thanks to the ruling. The whole situation has become a bit of a circus, of course, with strange things coming to light along the way, including Whole Foods CEO John Mackey's anonymous postings on the Internet, the resulting investigations into his behavior by the SEC and the company's board, and the FTC's accidental spillage of some confidential company information.

The FTC says it will appeal. That probably won't surprise anybody, given the agency's zeal so far in fighting this particular deal.

Still, Judge Friedman's opinion on the matter -- which reportedly ran 93 pages and remains under seal to protect confidential information about the companies -- supports what many of us have believed to be true about this deal: Whole Foods competes with many formidable competitors that are dabbling in organics and gourmet offerings on varying scales. The list includes well-known names such as Safeway (NYSE:SWY), Kroger (NYSE:KR), and Trader Joe's, and it even extends down to Mom-and-Pop natural-food stores. (Kroger, in fact, said recently that it's stepping up its organic fare.)  

Wild Oats just doesn't have that much of an impact on Whole Foods' business, competitively speaking.

Many of us were disturbed by Mackey's anonymous postings on Yahoo!'s discussion boards, and that situation still has to be addressed, since the SEC and Whole Foods' board of directors are both investigating his behavior. Despite these elements, though, I'm in the camp that still believes Whole Foods is a solid company for the long term. Although I originally wondered what the company might become in the event that Mackey is forced to step down, I've come around to the idea that he does have a competent and tenured management team on board, one that surely shares his strategy and vision. So whether he stays or says sayonara, the grocer has an extremely bright future either way.

That said, there are still some issues to iron out, such as what the SEC and the company's board will decide about Mackey's behavior. The FTC's appeal could prolong things and cause more headaches, too, despite this current victory. And even with what appears to be greater chances that the two companies will be allowed to go forward with their plans, let's not forget that acquiring a company isn't a magic bullet. There will be a lot of work to do as the two companies combine, since Wild Oats is a larger company than the ones Whole Foods has traditionally acquired.

Regardless, though, the closer these situations come to resolution (and Judge Friedman's decision seems like a significant step in that direction), the sooner Whole Foods will be able to get back to business as usual. And that's good news for the company's long-term shareholders.

Whole Foods Market is a Motley Fool Stock Advisor recommendation. To find out what other companies David and Tom Gardner have recommended to subscribers, take a 30-day free trial.

Alyce Lomax owns shares of Whole Foods Market. The Fool has a tasty disclosure policy.