It’s not the end of online access to Jon Stewart and Stephen Colbert but next week tracking them down may be a little less convenient for those used to watching on Hulu. Viacom (NYSE: VIA) is removing Comedy Central from the ad-supported video portal at 11:59 p.m. March 9 after a 21-month run. It’s the first major content defection for Hulu, the JV owned by Disney (NYSE: DIS), News Corp (NYSE: NWS). NBC Universal (NYSE: GE) and Prividence Equity. The site announced the move Tuesday afternoon in a corporate blog post by Andy Forssell, SVP of content & distribution for Hulu, telling users how they could find their faves after that (TheDailyShow.com and ColbertNation.com) and explaining:

“In the past 21 months, we’ve had very strong results for both Hulu and Comedy Central, in terms of the views and revenue we’ve generated, thanks to a couple of key trends. First, more and more of our viewers have voted with their time by making these shows a regular part of their day. And second, we’ve driven steadily increasing revenue per view as advertisers voted with their budgets to take advantage of innovative ad formats and very strong advertising effectiveness. After a series of discussions with the team at Comedy Central, though, we ultimately were unable to secure the rights to extend these shows for a much longer period of time.”

The Hulu search engine will continue to track the shows with links directly to their respective sites—as it currently does with Southpark but the player experience varies considerably and Viacom will lose the promo effect of being highlighted on the front page of the highly popular site. Forssell was careful not to burn bridges and to suggest circumstances could change.

Comedy Central’s statement: “Comedy Central has made The Daily Show with Jon Stewart and The Colbert Report available to consumers through Hulu since June 2008.  ... Hulu was one of the many digital distribution partners we’ve worked with over the past few years to add new outlets for our valuable and powerful content and to help drive the businesses of our partners.  We had a great experience with Hulu, and we hope to work with its team again in the future.”

What happened? Step into Comedy Central’s shoes and ask if you’d be satisfied with a financial deal that matched those of networks bringing fewer episodes or shows without the Stewart/Colbert track record for destination viewing. Then try on a pair of Hulu sneaks and ask what you’re willing to do to keep them? Are you willing to tilt your business model to make a better deal based on quality or draw? How far will you go? The answer for now: not far enough to keep the assistant sports psychologist for U.S. speed skating on the roster.

This isn’t Disney and Cablevision (NYSE: CVC), where going dark with a distributor means subscribers who pay for access can no longer get it. If WABC goes off Cablevision Sunday, Oscar fans who get their signal from the operator will be scrambling for alternatives. But no one was paying Hulu to watch Comedy Central, no one has to miss a dose of Stewart or Colbert—and no one is throwing poison-tipped darts.

It is, though, a reminder of how reliant Hulu and other portals are on the content providers—one reason why Hulu’s arrangements with its own JV partners are so key. And one reason why Hulu is trying its hand at original programming like tonight’s premiere of If I Can Dream. It’s also a reminder of why Hulu needs to add a subscription model.

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