There's a few things to consider before teeing off on Square.
1. It's the launch of a new expansion. Same thing happens to WoW, GW2, etc, etc. The idea that these games should accommodate a 1-2 week surge in players doesn't really support the reality of the economics.
2. The servers experiencing the obscenely long wait times were offered free transfers off of the server to less populated servers. Not only were the transfers free, players got in-game rewards for transferring from an overpopulated world to a less populated one. SE made no secret that if you were on one of these worlds, you should expect long queues and transferring would be in your interest.
3. The importance of being on a "particular" server is pretty low for most players given the game has a "group finder" *and* a "party finder" that allows anyone in the same data center to group up for most of the game's content. Social would be the only concern. If your guild is important to you then you're probably close enough to coordinate everyone transfer to a less congested server. If you're one of the "single player" in an MMO players then it shouldn't matter.
4. The game isn't 4 years old. It was released in 2010. It got a major overhaul, but the very base of the game (engine, database, etc) is the same. The game was already in development in 2006 before easily scalable development platforms were in full swing.
5. Their decision to just log people off may or may not be the right one, but the alternative is ban people who set up something like a macro on a naga mouse or something similiar to move their character. It's even fairly simple to make an auto login macro on these devices.
tl;dr
Square took measures in accordance with the industry in regards to server congestion. Whether that should be acceptable or not industry wide is another thing.