I'd like to think that Amara does have some sort of connection/effect on Dean, I think that would tie in nicely to his journey this season and make the Darkness that much harder to deal with.

But I can also see that Dean has never warmed to 'good' supernatural beings; he's more of a black and white kinda guy, whereas Sam has seen shades of grey (especially in the early seasons). The comments you mentioned do seem particularly harsh, but I'm not sure at this point what to think...is is purposeful? Accidental? I'm sure looking forward to finding out!