Sage is emotionally fucked up, she's admitted that directly to the mc.
Love/hate - her emotions towards Chad are raw right now. Anyone who's suffered through the break up of a year+ long relationship knows how fucked that place is (unless you wanted out, then it's yippee!)...
When she thought Chad was cheating on her, she was just angry, she wanted to get a confession and to tear strips of him and the side bitch, then everything could go back to normal. She wasn't looking at ending the relationship, even if the mc was pushing her to.
Even though there was no chemistry ever depicted between Sage and Chad, they were together for long enough that the sudden, abrupt end of the relationship has sent her reeling.
She didn't want a complicated relationship with the mc, sex on the side was all it was meant to be (to make her feel desired, and to get back at Chad), but their chemistry was undeniable (how the fuck can a slide show porn game project such strong chemistry is beyond me, but ya'll know it's there, right?)
So she'd already formed quite a bond with the mc - I wouldn't call it love or anything, but they are fucking close (and I do mean "fucking"). At the same time, she hasn't even got over the break up with Chad, and combine all that with her family's shit emotional handling issues... maybe the mc was right to suggest they cool down for a bit.
All that said, I also hope we aren't forced into exposing Chad/Troy's secret. That'd be a seriously fucked up thing to be forced to do, and there's no taking it back once it's out there (all the other dumb shit the mc has done against our will has been fairly transient).
Nope, I can definitely say I have not thought of that possibility, and I'm still not thinking of that possibility right now!