Wyll should be furious when you agree to help Minthara - not after you finish killing all of the tieflings. He should ask you right away (or once Minthara is out of earshot) what your intentions are and, if you say that you're going to help Minthara, immediately leave the group, warn the tieflings, and fight on their side. You could tell him that you're actually planning to betray Minthara (which might involve a persuasion or deception check, depending on your intention) and then he'd play along.
Wait, hold on. I remember having exactly this conversation with Wyll, at exactly the point you mention, including the option to tell him you're setting Minthara up (which is what I was doing). Have you played that scene since the last patch?
