In light of the new info about the RJ not being fully parked I'd say:
Special aircraft require special treatment(both from pilot and ATC).AF skipper will take the blame but so must ATC.They knew an A380 was taxiing and should have ensured the RJ was FULLY parked before issuing clearance.If the RJ pilot didnt report fully parked then I still say its encumbent upon ATC to verify that he is clear before issuing "continue taxi" instruction.Only if the RJ pilot reports fully parked when he's not gets ATC clear off the hook.The 2 frequencies(ramp vs gnd) does cloud the issue but doesnt let ATC off the hook.Two aircraft in close proximity both talking on different freqs never works.Its up to ATC to cover that uncertainty.JFK controllers are slick but there are occasions when slickness is the wrong MO.Sometimes they need to slow down and be more circumspect.