I do think people bring up a legitimate issue when they address the possibility of fragmentation. One of the reasons I love my Ipad mini is there is such excellent software available for it, and one of the reasons it there is such excellent software available for it is it's easier for developers to write software for a single cohesive platform.
Having said, that, I'd offer three counterarguments.
1. I don't think that allowing users who wish to to re-install ios 6 would contribute that much to fragmentation. I don't think that many users would take advantage of it. After all it would be a chore. One has to wipe one's machine, and re-install everything from scratch. Furthermore, Apple could add additional hoops if it wished, such as a big button one had to press acknowledging that this was an obsolete version of the software, that it was no longer supported, that developers were no longer developing for it, and that Apple felt you would really be happier with their shiny new operating system.
I called up my brother after ios 7 came out and asked if he'd upgraded his iphone, and he didn't know. It turned out he had, he just care enough to notice. I suspect most users wouldn't bother to go to the trouble of installing the old os; it would likely be limited to people who had issues with older hardware or software, or who had very strong opinions about design aesthetics. And if I'm wrong, and a sizeable number of people did choose to stick with ios 6, that might be a sign there are issues Apple ought to address in ios 7.
2. While some people would re-install ios 6 given the opportunity, that would be mitigated by people who would upgrade, once they were confident it wasn't an irrevocable decision. Personally, I would install ios 7 today on my ipad, if I knew I could try it out for a couple weeks and revert back if I really didn't care for it.
3. While there might be costs to additional fragmentation, those costs would primarily be born by those who made the choice not to upgrade. Obviously, someone electing to use the older ios can't expect to get the new features of the new software, and can't expect developers to develop or upgrade software for what is now a minority platform. Presumably those people who make the decision not to upgrade have decided it is worth this cost.