Of course the smell will go away, given enough time. The question is exactly how long you can tolerate it, which only you can judge. Durian actually has a remarkably fascinating smell, featuring a huge range of aromatic compounds including some that haven't been identified in any other produce. (This link is unfortunately behind a paywall, and I haven't read the whole thing, but even the abstract gives an interesting glimpse.)
If you're concerned, take precautions. Open it outside, or in a room with plenty of ventilation. Put down paper or plastic sheeting to catch any juices or mess that might leave a lingering smell (as this helpful article suggests).
A couple of sources (such as this blog post, and somewhat more lucidly, this About.com article) suggest that by running hot water over the expended shell, you can create a mild solution which helps neutralize the smell. I can't vouch for the accuracy of this method but it's suggested in multiple places, so it seems unlikely to be a cruel prank.
There are actually other, more pressing concerns with durian. For instance, one study suggests that durian fruit breaks down some of the enzymes that your liver uses to neutralize the toxic byproducts of alcohol. It's apparently a bit of southeast Asian folk wisdom that drinking and durians do not mix, and more than one death has been blamed on the combination. So, don't worry about the smell. Worry about mixing tequila shots with durian instead.