I do agree with you that each characters reputations should count towards the "X number of exalted factions achievements". That would indeed "penalize" someone switching to another toon as their main. I was disappointed when I realized that it wouldn't work that way, as I'd went and gotten Tranquillen to exalted on my one remaining horde toon as most of my others have been transferred to Alliance.
However, I am very much against having reputations themselves being account wide. The point of playing other toons is that you need to do things to progress them yourself, which includes running dungeons, getting the necessary reps, etc etc. I wouldn't mind if they implemented something similar to the VP buff (which gives you 50% increased VP on other toons on that server once you have capped VP on one toon) for reputations, but they really should be kept to a per-toon basis.