True, but if widening the scope of a warrant ends up invading the privacy of others completely uninvolved with the investigation, it just isn't right. And that is where the government messed up.
I don't follow. The inference we're meant to draw here is that DOJ wanted pen/trap information for Edward Snowden --- one specific person very much the target of the investigation. And what this article communicates is that Lavabit had that capability, but deliberately chose not to make it available to DOJ.
The goverment is very, very good at bad PR. I don't think any institution in the world is as good at making people (who didn't previously care) hate them as the US govt is. Self-fulfilling prophecies, in a way. They think everbody hates them, so they react in a paranoid manner and violate the entire world's privacy and civil rights, and they're surprised (or feel vindicated, I suppose) when it is precisely that that makes people hate them.