If you're referring to when he goes batshit and starts to attack you, I feel like that's a different story. In a way you're putting him out of his misery, but you're also ending his journey...I mean sure, you feel bad about it, but given the alternative I feel like you're doing him a favor. i felt bad that I was destroying my only real friend and companion, but once I had experienced both endings and realized the implications of them, you kind of realize that Solaire, while an awesome bro, wants the ending that I didn't. He's looking for a gloriously, grossly incandescent sun, while I wish to usher in the age of dark and extinguish the light. I feel like it's more of a jerk move to have him help me throughout the game only to betray him at the end.
that was more ranty than I intended