This is not accurate. Zuffa has no formal ownership stake in mixedmartialarts.com. They are a major advertiser, however, and so you can take that to mean whatever you will. If advertising comprises a significant percentage of your revenue, the biggest advertiser does have significant clout. This is true in both digital and traditional media.
The .tv change was made to parallel the ufc, but was not indicative of anything more. Also, at the time, MMA.com was owned by a marketing company, as it still is today.
In addition to the advertising clout, Kirik has always maintained that he wanted to keep a pipeline of contact to fighters, special promotions and the management at the UFC after seeing the consequences Sherdog and FcFighter faced for being critical. It was a business decision and one he's caught a lot of heat for over the years, but it kept the site positioned as THE place for insider info for years, not coincidentally because of the number of Zuffa employees and allies who posted there over the years.
Roy did help the UFC design their new site though, which doesn't prove ownership as much as cronyism, which was fairly common in the insular pre-TUF MMA industry.