I've tried the PS2 version out on both a 4:3 and a 16:9 screen and it doesn't stretch.
Does the PS2 version have any "widescreen" options? If it doesn't (and I'm pretty sure it doesn't), then the game won't support widescreen. The PS2 has no way of knowing your TV's shape or resolution, nor is there a system-level setting for them, which means that in order for a PS2 game to support widescreen or progressive scan, you need to select these options manually from an ingame menu. Incidentally, very few PS2 games support either one.
If MGS2 isn't stretching on your TV, then I'm guessing your TV is set to zoom in on 4:3 images so that they fill the screen, cropping off the top and bottom. Of course it's also possible that it's stretching and you're not noticing.