Is it better to have a player application stretch the video or to use a resolution that matches the video file?
That's really a loaded question.  In general, the rest of your content is going to look better if you leave the computer at native resolution and let the computer scale the video.  If for example you have a video that is a slightly different size, then you would end up scaling to get the resolution setting and again to get the native resolution of the display.  The TV should be able to take into account more information about the exact display too, so I'd leave the computer at native resolution and let software scale it.