As it is now, a player can resign a 3-player game at the cost of having their 3-player ranking hurt more than an ordinary loss to their two opponents would.
There are circumstances where it would be nice to have the ability to suggest to one of your opponents that you both resign and cede the game to the other player -- in which case it would seem reasonable for this to count as an ordinary loss to that player. Two come to mind, one applies in a game I'm currently player as I type this: one player has an insurmountable lead. It would be nice to be able to give him the game and move on to another since the current one isn't that much fun for the other two of us. The other is cases in which one player has to leave (real life getting in the way of games...) and one of the others is hopelessly trailing.
In a similar vein, perhaps if a player in a three-player resigns when they have more victory points than their two opponents combined, perhaps the punishment should be lighter, since that's obviously real life interfering, rather than bad sportsmanship.