The most important reason not to feed in the viv is the potential for impaction if you have a substrate that can be swallowed. If you use something like newspaper, there is minimal risk of that. If you use tongs to feed, or handle your snake at times other than feeding time, he is unlikely to develop a feeding response. However, there are some advantages to feeding in a separate container as well. First off, it gives you a chance to handle the snake at least once a week, to check his health, measure him, check for parasites, and such. Also, it is a great time to clean the tank without having to constantly watch the snake to make sure it doesn't escape.
Personally, I've done both. My ball pythons both get fed in their vivs, because they won't eat anywhere else. My corns have been fed both in and out of their vivs, and both methods have worked for me.