From what I gathered, he was removed for not taking his seat after being asked several times by the cabin crew. I don't see a problem with that per se.
I don't have a problem with it either. Pray in your seat. Why should the rest of the passengers be held up, inconvenienced, or even frightened by you having to go through some ritual. Once you're on the plane sit down, strap in and shut up so we can get going.
I think it is time a line is drawn in the sand. Feel free to believe what you want, how you want, as long as the rituals of the practice don't interfere with the laws of the land, rules of an organization, or result in the injury of another. If the airline kicked him off for being a particular religion, then that is their bad, and should be punished. If his religion kept him from obeying the rules of the airline, then that is his bad. Especially, if he knew he had to pray at a certain time that conflicted with his flight.
Flying is a right not a privilege so the airline was within its rights. That said am I right that this was about two minutes? I've watched flight attendants gossiping among themselves when a passenger had a need longer than that. Putting a charitable construction on the man's actions, perhaps he needed to stand or he was looking for some privacy away from folks. Yet, his timing was very bad and he should have known that. The airline seems to me to have pulled the string a little fast. Would they have done that if it had been a Mom with a sick child? I've heard screaming kids drown out the "safety instructions" and no one said anything. Seems over zealous to me. Whether that zealotry had a religious dimension (i.e. bigotry) is impossible to tell from the facts in the article.
To answer the sit/stand question, Mincha, the afternoon prayer, consists of four parts: Ashrei, which can be said sitting or standing; Shmonei Esrei, which MUST be said standing; Tachanun, which has a part where sitting is preferable, but not absolutely necessary and another where you should stand; Aleinu, which must be said standing. During this month, Nissan, Tachanun is not said, so most of the prayers would have been said standing. That aside, I don't know the particular circumstances, but you can pray Mincha from noon until sunset and it takes about 10-15 minutes when praying without a quorum of ten. That being the case, it would be interesting to find out why he couldn't have found the time before or after the flight. For that matter, he could have prayed after the plane reached cruising altitude.
I should qualify my earlier post and add that during Shmonei Esrei you have to stand with your feet together. That may explain why he wouldn't have wanted to pray while in the air, in case of turbulence.