Quite... Perhpas it's for the better that you bend the Oddworld timeline to your will, to suit your style, rather than to bend sligs personalities. Regardless, it makes somewhat logical sense, although I doubt it merely happened overnight, so unless Marek's a very old slig, I find it slightly difficult to believe that he recalls when it was normal to beat mudokons... A lot of plot devices can be deployed to dempen that minor flaw though, and it really isn't all that big a problem.
Maybe it'd just me, but at the moment, the squad seems rather unalarmed.
Pointing out such little flaws only shows that there aren't any big flaws to point out, so consider my opinion to be a good one.