The point was that the state should jealously guard its powers so that it has the flexibility to enact policies that secure the long-term safety and welfare of its citizens, even if that comes at the literal expense of some, such as the Penn family.
The entire rebuttal is a bit long to repost, but essentially, Brick says Wittes is taking that statement of Franklin's as applying to the entirety of his letter when in fact "[t]he real context of the quote is actually a very small portion of that letter in which the authors are discussing the defensive needs of certain 'freemen' living on the frontiers, or 'backwoods' areas of the colony." Furthermore, Brick states that Franklin made very similar statements elsewhere where the meaning is very clear--and in line with the conventional pro-liberty understanding, not Wittes' pro-government-power understanding.
I would like to see some historians argue it out.
Even ignoring all the other paragraphs, in no way could the liberty imply the frontiersmen's individual freedom (or civil rights, as we would call them). The contended Bill doesn't encroach on the frontiersmen livelihood or freedoms; it's a Bill to raise money for their defense (it literally says that in the next sentence) by taxing proprietary estate holders, who are definitely not the same people as the frontiersmen. It doesn't effect the frontiersmen directly, except by providing for more consistent defense funding. It's a pretty difficult piece to work through and I wouldn't claim that I fully understand all that Franklin is arguing, but whatever he is saying there, it can't possibly be referring to individual freedom. There's not the slightest hint of such a connotation. Rather, whatever the precise point, it's clearly an equivocation of the Assembly's rights with those of the People.
Yeah, he uses that phrase again years later and the arguments are different in those contexts, but it's obviously a cool phrase. Of course he would repurpose it to suit whatever point he's trying to make.
For others' convenience, here's the whole thing: https://founders.archives.gov/documents/Franklin/01-06-02-01...