"afaik" there isnt really any difference between the game from a disk or thru steam, though I dont like steam and personally would never recommend using it. Anyway, its probably your system that cant really handle the game very well.
Did you patch it to the latest version, does the steam version even allow you to do that?

Get fraps and run it while you play to see what your FPS is during regular play. If its very poor than the above aplies and you would do good in investing in a beter system/upgrade.
http://www.fraps.com

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