So again, why not use the FISA court? That's why it's there, and nobody even know about it until much further down the line.
Why is the FISA court necessary? FISA is meant for surveillance of foreign intelligence agents inside the US (hence, the name - the Foreign Intelligence Surveillance Court). Of course, who is a "foreign intelligence agent" is open for debate.
I'm not a legal expert, but it would seem clear that there are no fourth amendment issues in searching a perp's phone. His house can be searched under a standard warrant, and his desk and safe and anything else specified on the warrant can be, too. Why not his phone?
The problem isn't with the law. It's with Apple confusing privacy rights and needs of national security. In the San Bernardino case, Apple was clearly wrong. There might have been a clear and present danger of further attacks which could have been discovered by searching his phone. It turns out there weren't, which was lucky. But imagine the outcry if another attack was linked to that one, and the attacks were coordinated by phones, and the FBI couldn't find out about it because they couldn't break into the attacker's phones, and Apple wouldn't help them, and many more people were killed as a result. In the Paris attacks, police found a number of phones, and they provided a lot of actionable information concerning the ISIS networks in France and Belgium and elsewhere, and that saved a lot of lives. If that attack happened in the US, would anyone here worry about searching attacker's phones?
Apple's rationale had some merit, in that if they could unlock his phone as the FBI wanted, others could, too. There are people in this world who know iPhone technology as well as Apple does, and they can certainly replicate whatever Apple would do to break into the phone. So, thinking that iPhones are impenetrable, even with encryption, is a fallacy.
But Apple had already done this sort of thing at the FBI's request, so they were being hypocritical in not doing it for this one phone. Or for other phones from criminals or terrorists, too. I'm all for privacy of phones and other property of individuals, but I'm also all for security of the populous in general. And that needs to take priority in many situations, and it's incumbent on vendors like Apple to assist in that.