I know where you are coming from, and it doesn't make this question less weird- stop this ship before it's too late! But in-game, if Estinien does love, it's what we call a brotherly love. Estinien and Alphinaud are full of shenanigans. You see how comfortable Estinien is with Alphinaud. This is probably because Estinien had a younger brother in childhood, who unfortunately died in the Nidhogg invasion. He may be projecting his brother onto Alphinaud and treats him as such, while Alphinaud sees him as a role model of endurance and persistence.