The issue is whether a court has the right to compel parties to furnish materials when they can. Search warrants are traditionally legal and sensible. There is no issue of self-incrimination here. What has changed is not the runaway power of the government, it is the changed nature and sheer quantity of information in the computer age. And the recent popularity of suicide shooters and bombers.
One subtlety here is that the owner of the phone isn't on trial - he's dead - but the desire by the FBI to track his contacts and possibly prevent more terrorist attacks.
If I were Cook, I'd find a way to do it. Dead suicide killers don't need Apple to defend their privacy.
"Life, liberty, the pursuit of happiness" lists "life" first.