still Kishi left himself room or space to pull explanation here why it couldn't work then... but can work now. These reasons are:
1) Back then Kyuubi was hostile... now Kurama wanted to save Naruto as his friend
2) Back then Kyuubi was 100% full size .... now it was just 50% of Kurama.
3) Back then Kyuubi was ripped out forcefully from Kushina... now it was ripped while Naruto was using Kurama as chakra avatar so maybe it was removed faster.
4) Back then sealing Kyuubi back could not save Kushina as Kyuubi was hostile and would do everything to escape and harm Kishina while now Kurama would do everything to be dragged into Naruto avoiding any harm to his body while healing it right away.
^^ these are my guesses
However I agree that removing Kurama from Minato and sealing it in Naruto would be asspull as Edo Tensei could not extract any chakra outside and transfer to someone other.
but wait... we still didn't know how Edo Tensei body containing external source of power in shape of bijuu work even...