Ok, first off, just to get it out of the way:
ZOMG!!! JON SHAVER IS TEH HITLAR!!!11!
There. Now we have Godwin fully covered.
Moving on to less intarwebzy subjects...
No it'd be a better analogy to say "like blaming Adolf Eichmann [OR TEH HITLZR!! LAWL]for the holocaust" (ok way out of proprotion still, but it's an analogy). He wasn't the head honcho, but as lead designer you have to assume that he either came up with most of the concepts himself or that his was the voice greenlighting the concepts. IF this is not the case then there has to be two questions asked:
1) Is the concept of leadership so meaningless to Firaxis/2K that they'll put anyone in charge, and
2) Why did Jon not jump ship when he realised that the job as just him as fall guy if it went wrong (which would be alot quicker than when he eventually left)?
Now I know we can't blame him for everything, e.g. all the job losses half way through, but there are a lot of things wrong with this game that no amount of programming can fix, i.e. the concepts from the start were wrong for the game and either should have not been considered, or dropped when realisation struck that they were wrong.
...ok, so maybe not TOTALLY done with intarwebzy bits.

(Just funnin' here, though, really.)
But seriously, I see your point, and agree with you to some extent.
Whether it's entirely his fault or not, he does bear SOME of the responsibility. That said, it strikes me that he was the wrong guy for the job, and someone ELSE bears the responsibility of putting him in that job in the first place, and therefore bears more responsibility for the state of Civ 5.
I think it's really a combination of factors. Yes, he is a guy who is relatively inexperienced (at least at leading software teams), and is primarily a modder. Modders can be good idea guys, but in terms of managing your team and getting them to effectively implement ideas with limited resources...that's a different set of skills altogether.
Given how the various changes to the game play out, I get the sneaking suspicion (and I, of course, have no proof of this) that the changes were handed down from on-high. The suits at 2K said "We want this list of features in the game, so that's your primary focus." Shafer delivered as best he could, and my hunch is that, especially when coupled with layoffs, he didn't have enough left to deal with other areas of the game, and was pretty much "just following orders." (Godwin? Is that you again? Will you get out of here already?!)
Anyway, yeah, I think he's responsible, but my sense is he was also hamstrung from the get-go. Does that mean that a really talented, experienced team leader couldn't still have pulled together a better product? Absolutely not. It would've been an uphill battle either way (oooh, those terrain bonuses...), but someone with more years/mileage in this particular type of position might've done a better job. Maybe not, though. We really can't know that without knowing the specifics.
Shafer, however, was not the right guy for this gig. That much is clear. Not necessarily a sleight against him (not unless he takes another Team Lead job), but neither does it totally absolve him of any responsibility. You put your name on the thing, you're responsible. Hey, he could've always gone the "Alan Smithee" approach.
The thing is, from some of the stories I've heard about how the software industry works....well, this stuff happens, and sometimes at the biggest of names where you'd think they know how to run a business better.
Two things:
1.) They DO know how to run a business better, but that business is the business of making money by any means available, rather than turning out quality product and hoping it makes money. If that means shafting a particular title with a tiny staff, a miniscule budget, and a check-list of "must have" features, well...they'll do it. Especially if they know that as long as the product is minimally functional and -- above all --
pretty, it'll sell based on its reputation alone.
2.) In some cases, former lead designers will "take a sabbatical" when they recognize the incoming no-win scenario, which can result in lesser experienced hands being promoted (hey, someone has to be Team Lead, right?), so even a well-run company can end up with an inexperience project lead.