Zoo and aquariums like SeaWorld have very important roles in this world. With destruction of habitat and entire species they serve to help preserve these animals when the "wild" is disappearing more and more every day. They also provide education and create empathy and interest in these animals that would never happen otherwise, inspiring people to care and do something to try and help the plight of all animals. SeaWorld is a victim of their own success. They made people care about killer whales so much that they now have to justify their keeping them. I don't want to see any animal suffer, and while I do believe keeping these animals in captivity is not ideal, they are well taken care of and kept as well as possible and they serve as valuable ambassadors of their species and all marine animals, which in the long run serves the greater good.
I also ask everyone to look at the information being put out there from the animal rights groups and really evaluate the scientific validity of what they say. So much of what they describe about the treatment of SeaWorld's animals is humans ascribing human emotions and feelings to animals that are not human. All their arguments about things like separating mothers and their offspring could easily be applied to cats and dogs, but no one gets upset about giving away puppies and kittens. They make arguments for sea pens for keeping these whales in larger more natural settings, but they don't have a solution for keeping those sea pens free from pollution, and want to charge people to come see the whales in those sea pens (just like they vilify SeaWorld for doing).
SeaWorld is a business, not a charity. They make money with those whales and the other animals in their care, but also provide education, chances to do research and help to wild life in return. Just like PETA and these other groups are businesses as well, and they are raking in money "fighting for animal rights", but their own track record for actually helping animals is shameful.