Upload & Sell: Off
The question of whether or not it's worth it depends on a few factors, the largest being the value of a 5 year warranty to you. I've been shooting Nikon on and off since 2005, and I've never sent a lens in for an issue that didn't involve ME (or a kid/wife) breaking it (ie, non-warranty), except a 80-200mm that needed it's AF/M ring adjusted - however that was a lens I'd bought used and was older then 5 years. If a lens is defective I can find out in a day of testing and send it back immediately. So - the 5 year warranty hasn't been worth that much to me, I'm willing to risk it.
However, a lens with a box sells used for more then one without one, and I'd bet a lens in a regular box would sell used for more then one in a refurb box (refurb lens boxes are plain brown and marked refurb). You're probably not going to be able to sell it used for as much unless you hang on to it long enough for it to not matter anymore (say a decade or two).
Basically I decide if the discount is worth it if it's greater then it's estimated depreciation from being a refurb. I just bought a refurb 28mm 1.8G for $600 instead of the normal $700 price. I'll make an assumption that a used version with a box would sell for $462 (2/3rd of retail). I bet I could get more then $362 for it used, therefore it was worth it to me.