Agnes’s fire doesn’t always burn.
In “Recluse” she kisses a boy on his cheek to free him from The Web. It doesn’t burn at first, then at just the right moment it scalds his face so bad that the fears powers over him break just enough to let him flee from Hilltop Road. In “Burning Desire” Jack tells us that he took Agnes’s order many times without incident. The first time he noticed something off was when a man approached her and she made him leave with sweat dripping down his forehead. After that Jack mentions he saw scorch marks on her chair for the first time.
So Agnes’s fire is more like a candle than a wildfire. It’s always lit but she seems to have some form of control over it. If she didn’t she would have burned the boy on Hilltop Road as bad as she did Jack and made him overheat while he took her coffee order.
But doesn’t that observation make the end of “Burning Desires” a bit more interesting? Agnes burns Jack so bad he’s hospitalized. Yet, it does seem like her powers are uncontrolled.
I think the darkest interpretation is that Agnes might have burned Jack on purpose. Either so that he always carried a reminder of her with him, or as a sacrifice to The Desolation since in the end she did feel a duty towards it, and burning Jack could represent the idea of her ever having a normal life falling into pieces.
But I think the interpretation I believe much more than that is that Agnes’s desire for Jack (And an unburdened life) was so strong that she couldn’t control herself. The fire that she usually could keep tempered burned out of control in her grief for herself and what she was loosing, until she was the victim of the desolation she was supposed to cause the world.