Weh weh weh.
Would you like some cheese with your whine, Bungie?
So sorry that you're faced with having to do some engineering when a major OS update comes out and you'd really rather be doing fun new games. You must be the only company ever to find themselves in a situation like this. Suck it up, stop blaming the user, and fix your game.
Halo 2 had this exact same problem when you 'installed it to the hard drive'. The root cause was that it used a teeny-tiny block size when copying maps over. It would read a teeny-tiny amount, then immediately write it to the cache partition, then read the next teeny-tiny amount. Ostensibly this was because the Xbox only had 64MB to play in, but really it was so that the game would run well off the DVD, but mysteriously break off the hard disk. The reason, of course, being that reading from and writing to different devices means that most of the million seeks are to a place the heads are already at, but reading from and writing to the same device means it has to actually perform them and gets clobbered.
There's no reason Halo 3 has to be modified in any kind of hacky, 'detect and catch the corner-cases'way; all it needs to do is instead of reading a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, then writing a half-k or so, then reading a half-k or so, then writing a half-k or so, simply use a bigger buffer the exact way Halo:CE did.
I mean, you could do a benchmarked mad thrash-copy to work out whether you're running off the hard disk* (or a straight benchmarked read to work out if the device you're running off is fast enough to not need the cache), and then copy or not copy maps**, but there's no real point in doing so when you can just use a sensible buffer size like every other program in the known universe***. Copying files is not hard.
Getting a few million people to change their mind 'for the good of the community' is hard.
* the way the new OS implements the HD install is to use a disk image to emulate running off the disk, so the game can't just ask if it's on the hard disk or not
** Another solution would be to release a 'Halo 3 maps on your hard disk' bit of DLC: Halo doesn't cache DLC maps, because it can tell that they're already on the hard disk.
*** Does Windows go batshit when you (copy c:\large_file c:\copy_of_large_file)? No it does not.