I would assume that at a guild's max level reputation would be earned in the same way that 'gives xp or honor' talents currently work. That it checks if normally the guild would have gotten xp for the action, and if so, regardless of whether the guild actually did gain xp the reputation is given.
And wow, some of those perks are really really really nice. I mean guild mail, omg, I've wanted that so much at times. And just the passive stuff like +x% honor, flasks, material gathering, extra gold put into guild bank, speed, rep (DO WANT!!!) is just so nice.
lift of cataclysm NDA
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