Maybe the thinking at Square Enix was, Tomb Raider will never be as big as the Uncharted series unless they went exclusive. Also, 110% sure that Microsoft had to pay for this one, but that isn't really news, now is it? This can happen, and Sony can do the same for any other future third party game coming down the pipeline. This isn't 'evil' of MS or Square Enix, it's just business; there's nothing immoral or unethical about it at all.
Sure, fans of TR on Sony platforms are going to be upset. But that's console wars. If another game was announced third-party full exclusive to Playstation, this would be a different thread with Xbox owners lamenting it and Sony owners rubbing it in their faces...In the end, i think these companies don't think of the gamers when they make these decisions, they think of the money (which is how business is supposed to work anyway) and people should just get used to it.
Going back to my point about Tomb Raider trying to reach the same levels of fame as the Uncharted series, going full exclusive with one platform is a big risk but it has potentially high returns, only if Microsoft is going to push Lara Croft as a character that belongs on Xbox. If they co-market this and spend on marketing for it instead of Square Enix, it can be as big as Uncharted. It all depends on timing (no other major triple A releases on the same / competing platforms during the same time frame), and messaging (selling the game just like they sell Halo or Forza or Gears) if they want Tomb Raider to stay exclusive. Otherwise, it would be money wasted for Microsoft if TR doesn't do well on a single platform, and then we'll see it on the other platforms immediately after that.