I was going to say that the original meaning doesn't take anything away from the quote as currently used and the power of that meaning. But Wittes already said that too, in the article you linked:
> "... maybe it doesn't matter so much what Franklin was actually trying to say because the quotation means so much to us in terms of the tension between government power and individual liberties."
I also disagree with Wittes that this means "not quite the opposite... but closer to the opposite [than the usual usage today]."
Franklin was arguing that the state ought to have the right to tax in order to defend the territory on the public's behalf. The Penns were trying to offer a one-time fee in exchange for not being taxed going forward.
Thus, Franklin's implication seems to be: do not trade temporary security in exchange for long-term liberty.
And so, I think the quote's modern usage and its originally intended meaning are very much in alignment. Just as the Penns offered a short-term benefit to security in exchange for a longer-term loss to prospective liberty, the FBI here is offering a short-term benefit (of debatable potential) to security by disallowing encryption or having master keys/backdoors, in exchange for a longer-term loss to prospective liberty.
It seems to me Wittes (and the NPR reporting) just isn't thinking about it deeply enough. It's not as simple as "oh, Franklin was original discussing a security matter and arguing for the state to provide security"... in fact, it is more nuanced and Franklin was saying that the state (and the public) should not accept, let alone advocate for, short-term security at the cost of long-term liberty and security.