I'd be far more worried by a mechanically good system with the same racist/sexist ideology.
I wouldn't, most DMs I've had homebrew, and if they're going to use a setting and make use of its racist/sexist ideology then they're probably already doing with another system.
A REAL bad system would be both good AND tie in sexism/racism into the system so that you COULDN'T untie it (for instance maybe evil is a stat that influences combat ability and grants stuff like horns or a damaging evil aura, and then tied into yet ANOTHER mechanic that makes removing it destructive to the system).
Evil to some extent DOES have influence in DnD/PF due to spells that affect good and evil differently, but it's still pretty limited. What I'm talking about would probably be something like evil is the strongest modifier to strength while good is the strongest modifier to constitution, whilst some skills SPECIFICALLY only benefit from the evil or good modifier to that stat or something. EDIT: Oh, and race would affect the good/evil thing by perhaps some races being naturally gifted with the good stat and bad races with the evil stat, perhaps based on hues of skin color can increase said stat? He apparently already has a table for every point of gale strength.
As to the orcs situation, I can't seem to find where I read that there were peaceful orcs (my memory must be playing tricks on me). As for how orcs are created, I was under the assumption they were elves called back from the dead or created in some other way, not born (I didn't read the book and haven't seen the movies in ages).