People with disabilities are consistently fighting for equal rights throughout the world, so yes they should be allowed to play on major league sports. It was nice that people created the special olympics, but if a person is talented enough to play the sport then they should be allowed to at least try out for the team.
As long as a person is capable of playing their sport at the highest level, that individual should be allowed to play. Some physical disabilities are not visible. There are people who grow up with arthritis, hearing disorders, and other physical disabilities which do not prevent them from being successful players in any sport. Suggesting all people with physical disabilities should be prevented from playing pro sports indicates a sort of privilege and disrespect for those who suffer any form of disability.
People with physical disabilities be allowed to play on major league sports teams so long as they can play the sport at the level needed to be a professional player. Some physical disabilites may not impede a person from playing certain sports, such as a deafness. Derrick Coleman is an American football player who is deaf, but his having a disability did not impede him from playing in a major league.
Technology hasn't caught up to the disabled but it is pushing that way. Eventually sports leagues, teams and associations will have to come up rules about allowing certain disabled people with specific bionic replacements. They will have to ask about the fairness of that person's ability to compete with "natural" people, such as that scissors man who was arrested. But currently, a disabled person couldn't hold his or her own in a American football game. A person missing two arms can't play baseball, but until technology gives that person new arms, new legs, a new spinal column, the current status would have to suffice. The next question will be: is it fair for someone to compete against a bionic person? What will prevent professional players from cutting off limbs to enhance their own abilities, or chances? (Much like steroids.)