Within the social sciences, researchers have to seek ethical approval for any experimentation they undertake, and a key part of this consent. OKCupid carried out research on people without their consent and clearly manipulated their life experiences. This would not be acceptable for social science researchers and should not be acceptable for social media and dating sites.
Online dating is a hit or miss. If you're genuine, it could work, but if you try to portray yourself as something else then it won't. With that being said, it's in a website's best interest to find out what kind of people are using their product and if someone is being fake then it's going to throw off their research.
I don't think they went too far. Only one of the three experiments was conducted without user's knowledge. All they did was reverse the compatibility rating for a (what I assume) small sample out of their users. I doubt it impacted any of the users involved in a negative emotional or physical way.
Yes, the experiment is acceptable. They were trying to see if their theory was correct. People just look at pictures is what they say so using math to connect people they fell is a better way to meet your true love. With the experiment they mixed up people who should of been placed together to see if that worked also. They had better matched with their first theory.