I don't think her line should be taken that lightly when she bothered saying it out loud and it did actually hold some kind of meaning even back when they had no idea about the truth of the outside world (especially when it later turned out that Eren, one of Ymir's many subjects who holds the power to control them, actually positioned himself as an enemy of humanity and is threatening said humanity with the Rumbling which could potentially destroy the world).
Just like her following claim of being humanity's enemy (but Eren's ally), it served not only as a way to completely divorce herself from the role of messiah her father was trying to push onto her, but also as a way to relieve her friend of the anguish he felt over his father's actions, the countless sacrifices made for his sake or because of him and his own perceived absence of value, as someone who in the end was just a mistake and whose grand ambitions were completely devoid of meaning.
Historia herself most likely didn't think that far (because like Utgard the adreline just made her say what was on her mind without any kind of filter), but she basically dragged Eren out of his pit of despair by completely downplaying the "mission" he once gave himself (saving humanity, killing all the titans) so that the words he needed to hear would actually reach him.
Even beyond all that shit I just wrote SnK remains a fictional work, not real life. Events don't happen at random and lines aren't said at random either, especially for a manga like this one. If a character says or thinks something, especially in a character moment as pivotal as that one, there's a 100% chance there's meaning to it.