Thats a nice theory, but there's no evidence that they were built that way to resist gunfire. I posed the question to some colleagues who work or have worked at NAVSEA on various survivability projects, and who also have a deep interest in US naval history. Here's what I heard back from one of them (I got several replies all along the same lines, but this was the most comprehensive)

"I have been a student of frigates of the sailing navies for over 40 years and have a huge collection of material for the US, Britain, and French frigaes of the period. I would not agree with the overall flow of the argument at all, I do not agree that the US design was an attempt to make a mini "ship" of the line, and would never agree that the US frigates were built to resist cannon shot of any size.

Their is little doubt in my mind that the design was an attempt to make very fast frigate that better armed that the standard frigates around the world. The USN was going to get six ships - every possible opponent would have access to considerably more vessels including ships of the line. Traditionally, ships of the line could out sail frigates in rough weather. If these ships were to survive, they needed to be seaworthy enough to out sail the ships they could not fight and, at the same time, defeat any ship that might catch them. They were built to the same concept that the German armoured ships were in prior to WWII.

The large US frigates were overbuilt to ensure that could both carry the rig and sails necesary to move them at high speeds, and the weight of metal necessary to defeat any oposing frigate they might find themselves fighting. Certainly the demise of USS President to a squadron of frigates established that ships were not invulnerable to cannon balls from frigate sized guns - but of course, they were never intended to be. Rather, the design gave the ships' the structural integrity to "take a licling and keep on ticking" when in action as well as the ability to carry an then extraordinary brioadside weight of metal without that weight ultimately hampering the ship's ability to sail at high speed in even heavy weather over time.

Thus, virtually every component in the design was "overbuilt" - the hull frame and fittings, planking, deck, masts, spars, and rigging were all bigger, thicker, and tougher than those of their smaller relatives in foreign navies only because that is was was required to make the design successful while giving the vessels long lifetime, and thus justifying the considerably expense their building set back the naval appropriations and the US treasury."

So, in summary, whilst the ships sides were undoubtedly heavily built they were that way because that was what was required to support the armament, and rig, not to resist gunfire. that was a happy by-product.