Very disappointing news. Glad I grabbed AM2R last night. That said, the overwhelming majority of companies would have done the same thing Nintendo did here. Heck, what Nintendo did here is pretty tame compared to what some other gaming companies would've done.
Sega and Valve are the exception, not the rule. And even in Black Mesa's case, the devs were required to make a few changes to the game.
If a company owns an IP, then they are within their rights to take necessary steps to protect that IP. It's that simple. That said, a tiny percentage of companies will evaluate fan projects on a case-by-case basis and make a judgement call on whether to put a stop to it or look the other way. Particularly companies smart enough to think outside the box and see the big picture. (A good fan project can help strengthen or revitalize an IP.) OTOH, the vast majority of videogame devs/pubs probably have a near-zero tolerance policy on fan projects using their IPs.
Nintendo has likely known about AM2R for quite some time. But when it got a lot of attention recently, it was inevitable and obvious that they would act with the takedowns.