Couldn't Kabuto have un-summoned Itachi?
The most plausible explanation is that the un-summoning with the empty coffin popping-up is only possible when the summoned is under the caster's control. Itachi broke free of Kabuto's control with the Kotoamatsukami, but he never broke free of the Edo Tensei itself (unlike what Deidara's answer suggests). This is why he could not be un-summoned (with the coffin), but was freed when the jutsu was undone.
Still, Kabuto could've undone the technique altogether, at the cost of un-summoning every shinobi he had summoned. However, this could mean a complete turnaround in the war. Anyway, Kabuto, most likely, did not think a complete release of the jutsu was needed, since was arrogant and confident that he could beat Itachi.