I don't code games so I can only speculate, and I also don't give a damn about customizable controls, but I don't think the give reason is accurate. Whether it was just told to us as a reason, or a developer told it as an excuse or something else, I don't buy it. Surely they are already only sending inputs over and not the actual button. I mean, I guess they could be for some reason I don't know of, but that's like the main gist of object oriented programming and wouldn't make sense to send the key, just the action. More realistically, I feel it just takes up more time for creating and testing as well as more possible breakin points. Right now the schemes are probably in some settings and config file, and the interface for choosing the schemes in game is for the most part static. Making the controls customizable would require an additional code layer to handle the mapping as well as the interface to do it, which in turn changes it from mostly static. It's not really a matter of how easy it is or not but what the priority of things are compared to other tasks. At the beginning, they map out everything they want to do and smaller things get left behind. Its not like its not doable, its just not important on their end, especially with it probably being a far less wanted feature. But yeah, if it was widely wanted and they wanted to do it it, it'd happen. I feel its completely reasonable its not in.
This is all just speculation on what I think really happened with it. I really don't know anything about how the animation systems work though in Halo games and Halo 4 could be even different and what Frank said could very well be true. Maybe Fyrewulff or Computron or someone that knows more about this stuff can comment.
That all said, I am pretty bummed by the schemes. All of them are almost there but off by a button or 2 in such a way that it won't be nearly as comfortable to play, and this seems to be echoed by many. It seems like even 2-3 more schemes would appease most people, and 5 would probably get everyone. I never expected or wanted customizable control schemes, but I think having tons of preset schemes is/would have been reasonable.
Since you sound like one of the few here that has some understanding of programming, and have been quite gentlemanly with my criticisms, you should check out David Aldridge's GDC 2011 presentation on Halo: Reach's gameplay networking. Really enlightening and in some cases, ingenius.
I Shot You First: Networking the Gameplay of HALO: REACH
There are actually quite a few coders in HaloGAF. Me, thezerofire, Karl, Zeoterlimits, Der Flatulator, Tashi, Bobs, Fyrewulff, Hydranockz, and Louis Wu are the ones I remember.