I think, as a society, it boils down to this: "And while the government may argue that its use would be limited to this case, there is no way to guarantee such control."

Can a private, for profit, company deny the will of an elected government working to solve a heinous crime based not on what they say they will do but because they cannot give a 100% guarantee that this is the only time/way it'll be used? Apple acknowledges that the government is saying it's limited to this case but because there's no guarantee (100% certainty) they feel they can deny it?

If yes, what does that mean as a broader precedent. Are we comfortable with private companies denying an elected government based not on what they agree to, but instead because there's a chance it'll be used in other ways?

As terribly flawed one might feel about government very few would think it has less accountability than a private company.