Hey dude, are you still with that problem? I've just installed MGS 1 (PC version) and I noticed too that my gamepad didn't work well at all, even I had the same problem, Snake didn't stop running like an idiot, without pressing any key of my gamepad...
You've got to download a little program called JoyToKey, and then configure it depending on your gamepad. I've just tried it and it works perfect for me. There are some tutorials out there that shows you how to configure the program.
Also, I think there's no way to disable your gamepad in the game, so if you want it to work well, you must "unassign" your gampad keys to avoid Snake running... (go to Options -> Controller Options, there), it should look like this: http://img4.imageshack.us/img4/8881/mgsconfig.gif
I'd like to know if it worked for you, tell me if there's something wrong... Cheers!