Well, it is heavily implied that Rayman made peace with most of his enemies after Rayman 1, and the end of Rayman Junior directly states that reformed antitoons, explorers and hunters attended the celebrations with no hard feelings. Then in Rayman Activity Centre some of the enemies from the first game appear as friends.
I see it as the 'people' who were enemies in R1 (livingstones, hunters, clowns, etc) were just normal people who fell under Mr Dark's spell like the boss enemies (So I doubt he would want to actually kill them), while the antitoons and obstacles like those spiky crystal ball things and those pointy stone rockets appeared as a result of the Valley falling into chaos.
Though livingstones can be made to fall into water, so I don't know what happens to them if that happens. As for Rayman punching antitoon's eyeballs out of their sockets, well, I'm not exactly sure what to make of that! Perhaps electoons are very magical beings who don't follow all laws of what's normal, and antitoons are just the evil equivalent of that.
Also, another headcanon! Rayman knows the name of every electoon and can recognise each one of them individually. All 714 (or more). And, he is confused as to why everyone else finds it so hard to tell them apart and remember all their names, yet he sometimes gets Globox's children confused with each other.