Last month, rumors hit the Web that TweetDeck, the multi-columned, much-preferred desktop client of hardcore users, had been acquired by Twitter. Today, TechCrunch is reporting that the deal has gone through, with Twitter snapping up the company for $40 to $50 million.

While we don’t want to be melodramatic, we’re afraid that this deal could be the beginning of the end and here’s why.

TweetDeck, It Was Nice To Know You…

The first, and most surface-level concern, is that Twitter will simply buy TweetDeck and shut it down. It wouldn’t be the first time that a big company has snatched up the competition to merely put it out of business. And Twitter has a number of reasons to do just that.

In March, Twitter director of platform Ryan Sarver advised developers to quit building clients, as this was an area that the company intended on moving into in an effort to give users a uniform experience. Allowing users to view tweets alongside Facebook and LinkedIn updates, as well as sending tweets longer than 140 characters using Deck.ly, certainly doesn’t sound like “uniform experience” to us, which brings us to our second point.

Where Art Thou, Facebook & LinkedIn Integration?

TweetDeck goes beyond Twitter, allowing users to track their Twitter, Facebook, Foursquare, LinkedIn, Myspace and Google Buzz accounts all on one dashboard. Even if Twitter allows TweetDeck to continue on as a desktop client, there’s no way Twitter is keeping the ability to track other services in the now-Twitter-owned client, right?

Right.

A N00bified TweetDeck Wouldn’t Be TweetDeck at All

As we mentioned before, TweetDeck is generally the Twitter client of choice for the hardcore Twitter user, but this hasn’t exactly been Twitter’s focus, as of late. The general push for Twitter has been to portray the service as something that’s good for anyone and everyone. TweetDeck is the opposite of a tool for new users. It has complicated settings and allows the end user to customize the experience greatly, setting up filters, custom columns and more.

Could they be making a play at being able to own the advanced user experience? Sure. More likely, the company is simply playing defense against UberMedia, which had reportedly bought TweetDeck last February. The deal would have given UberMedia control of nearly 20% of the Twitter client ecosystem, something Twitter certainly wasn’t keen on.

What Happens If Twitter Kills TweetDeck?

When the news first hit about Twitter potentially acquiring TweetDeck last month, Mrinal Desai wrote a guest post on TechCrunch discussing the various reasons that Twitter will kill TweetDeck upon completing the purchase. Desai points to many of the same issues discussed here and comes to a singular conclusion: “If Twitter does end up buying Tweetdeck, the product as we know it is a goner.”

But what happens then? Will Tweetdeck’s many dedicated users simply switch over to Twitter.com? Would Twitter force a Web-only experience and bring TweetDeck’s Chrome client to its Web experience? Or would Twitter turn TweetDeck into a pared down, paid product in an attempt to bring in revenue from its most hardcore users?

We don’t know, but we know one thing – a Twitter acquisition of TweetDeck does not look like a promising move for the end user, but we’re hoping for the best.