I think people have the FBIs motivations misunderstood. And I don't mean in some evil conspiracy theory sort of way, but in one that is pretty consistent with their mission.
Their main mission nowadays is to stop terrorism, etc... I I think that when they look at this rationally they believe are better served by being able to access these conversations.
The article theorizes that people with data to hide will use encryption, or otherwise would be so stupid, that one can find them easily in any case. In the real world a lot of these cases are broken on a "lucky" break or two. Someone improperly or not using their encryption software once, for example.
I think it seems foolish to accuse them of being dumb, evil, or incompetent. Given the stakes they deal with, and the amount of data they have to sift through, I think its very reasonable that they try to reduce the amount of work they need to do to find credible leads. And I'm sure they try to institute methods to minimize abuse, but I'm sure they are also aware that some abuse will happen.
While some of this feels like it may cross the line, I think it's a line that a rationale organization, with their mission, should push against.