I dunno. I do remember hearing that it was named after CV-6 even before Memory Alpha came into existence, but darned if I can remember where from.
I remember this as well, with the understanding that it was a better sell since the Enterprise had far more exploits than the Yorktown (not that the Yorktown was lacking in it's own exploits), but I cannot remember where I had hear that either.
Anywho, just to put in my two cents about the original argument, I don't know what the original name of the ship would have been (though I admit I do tend to go with Yorktown), but I favor the idea of renaming another Constitution class ship for a couple reasons:
There is no reason to not believe that there were other interim ships between the old connies and new excelsiors. ST6 occured 50 years after the Constitution was created, there had to be more ships in the meantime. Having said that ships are going to be created out of necessity, so if there are plenty of connies and/or more on the way, they may not have the need for another variation of flagship design. However I do not believe they would continue building the ships 50 years later, you never hear of a 50 year old design still being built but with all new tech, a new design that better fits the new tech will be created, and in the mean time, the old is refitted to keep up the numbers until the newer design can fully replace it. That sort of thing is happening now, for example F-16Cs are being refitted with new tech to keep them in service until all the bugs are ironed with the F-35, but although a newer design of the F-16 is available, they do not serve in the US because it is easier to keep the current fleet flying then throw them away and start with an all new fleet when you are waiting on a whole 'nother fleet anyway.
Also, I find it really hard to believe they would put so much effort into building a whole new ship and then decommission it a couple years later. If the design/tech were still viable, it would still be used, regardless of replacement by a modern design. This still leaves open the comment by Kirk in his log at the end of ST6 that another crew would continue, though it is uncertain if he means that the command crew would be decommissioned and the ship would continue, or if the new crew meant the next incarnation of enterprise, with a new crew (E-B and Harriman's crew).
Also, some things to think about
-Just because visual asthetics make ships look similar, it does not mean it is the same technology. For example, the Curry kitbash on DS9 was a Exselsior design with connie engines, but that does not mean that they are the same engines as the connie (they would have been, in fact, too large for the connie). The New Orleans class had similar design asthetics as the Galaxy class, but it was noted several times that the latter was more advanced than the former (the Galaxy class had a whole new designed engine system, noted various times on screen, which would have to differ even from the Nebula class, which would have been the most similar).
-Keep in mind that just because the ship was renamed for Kirk, doesn't mean the ship was built for Kirk. It could have easily been a ship awaiting decommission, but being the only available ship laying around, it could have been hurredly refitted into working condition (which in turn ended up botched) and then renamed for posterity.
-Book series are very unreliable. I tend to lean toward tech manual type stuff from official sources rather than "authorized works" from fan authors. Neither are any more canon than the other, but at least the former are more reliable sources.
-The thought of the Yorktown being named by Roddenberry is a big issue here. Keep in mind that there was more thought put into it than just the ravings of a man whose creation exceeded his reach, otherwise it likely would not have ended up in places like the TNG tech manual: "Gene Roddenberry, in a nod to his original name choice from 1964, suggested that the Yorktown was renamed USS Enterprise-A at the end of Star Trek IV, explaining why the latter ship seemed to be launched so quickly at the end of the movie. The Next Generation fourth season writer's technical manual also indicated this to be the case. This was further validated when, in the Encyclopedia, Mike Okuda described the Yorktown in 2293 as the second ship to bear this name."
-About Connies making it into the 24th century, there is an unreliable though technically canon onscreen anser: "At least one unnamed Constitution-class vessel participated in the Battle of Wolf 359 in 2366. Wreckage of the vessel or vessels was seen there as the USS Enterprise-D passed through the "grave yard" of ships that were defeated in the battle." -http://en.memory-alpha.org/wiki/Unnamed_Constitution_class_starships
Ok ok, my ranting is over. The truth is it is all 100% opinion, and each is going to believe whatever they believe regardless of what anyone says.