You can change the controls in the dos version. I prefer going through the config file directly rather than setup these days. One common problem to look out for is mapping multiple actions to the same key, make sure that if you mapped w to move forward, a to straff left, s to move back, and d to straff right that these keys arn't mapped to anything else.
Since you don't seem to have any nostalgia for the original game though, why not save yourself some grief and get eduke32. The aiming/mouse-look in it is much nicer, and iirc the keys have a modern mapping by default.