Was what Helena had said her true thoughts? Did the Deep Sea Church genuinely wish to establish communication with the Homeloss just for the sake of it? Did the "Spokesperson of God" truly believe in Captain Duncan's humanity and rationality as she claimed?
Duncan in fact dared not fully trust her, although the Female Pope appeared to be quite frank. Duncan was quite aware himself – he knew Homeloss had a renowned reputation and a distinguished "record of victories"; such fame meant that leaders like Helena would never deal with him without any reservations - she must have her guards up.
But having reservations might not be a bad thing; choosing to cooperate despite those reservations meant she had compelling reasons to do so. Perhaps it was the will of God, perhaps it was for the Church's benefit; whatever the reason was, the olive branch she extended now was real.