The context doesn't make what Franklin meant any different.
He wasn't warning against the dangers of giving up one's rights to the creeping authoritarianism of the state, he was complaining that people were giving up the "essential Liberty" provided by an effective Federal government for the "temporary safety" purchased by refusing to fund it.
Or to quote from the NPR article, "(...) far from being a pro-privacy quotation, if anything, it's a pro-taxation and pro-defense spending quotation."
Interestingly enough, the context is being used here to invert the meaning of Franklin's beliefs, rather than clarify them.