I may have misunderstood, so allow me to ask this:
Will the new 5.2 dailies not grant reputation to the new factions? Will it ONLY be through killing bosses in the raid?
There's a daily faction and there's a raid faction. You'll receive reputation from dailies for the daily faction (Sunreaver Onslaught). You can only increase reputation with the raid faction (Shado-Pan Assault) by raiding Throne of Thunder.
Does the daily faction also have gear?