If Lavabit refused, some random scapegoat within Lavabit (like, say the CEO, or whoever is deemed as the scapegoat) might get arrested, Lavabit would probably be ordered to close, and our lives wouldn't be affected too much. They're a tiny startup. They can be bullied quite easily without affecting national peace.

If Apple were ordered to close in an instant, there would be mass upheaval, unrest, protests, and huge economic losses just because of the sheer number of people that depend on their products on a daily basis for mission-critical things. Violence would break out. We might even end up facing nothing short of a civil war, and the federal government probably wouldn't want to risk that.