Doc was only doing his job, people.
As he put it, he had "a business to run." I mean, if you think about how much sawing off half a torso and splicing two sets of legs together would cost, could you really blame the guy for... you know... charging money?
Let us not forget that the Industrialists aren't "evil," they just have a different view point than the heroes of the Oddworld games. It's always been that way.
And I don't think Doc "knew" Stranger from some previous encounter; he was only makin' a livin'.