"If I stray in my remarks, I ask that you trust my judgement..." not sure where he did...which leaves what we didn't hear.
I don't think it is a matter of there being a darker side to him so much that it plays to a tragic flaw. Right now, the only people we know are resolved to save Estinien now are our character and Alphinaud. Unless this was stated earlier in heavensward, I think Aymeric doesn't know of this.
Right now, the Nidhogg possesed Estinien offers a tempting target: peace cannot be earned while Nidhoog lives. by killing him and making it clear he is dead, Aymeric gains the peace with the dragons, silence from dissenters, and Ishgard's freedom from the Dragonsong war. Literally everything to gain for him and those interested in those goals, and so little to lose.
all Aymeric needs to do is kill one angry, vengeful, dragon possessed friend already out for his hide to get it.
in contrast, Alphinaud and the main character's reason for saving Estinien are personal and complex, he is a friend, and having seen enough friends die to our enemies, we don't want to abandon him to the monsterous Nidhogg. We're not even sure of how, only that we must try.
Unless someone gives up here, this is a plot powder keg dying to go off.
