I think if he had been hurt in some way, he would've been one of the many "disappeared" children--lisa Irwin, DeOrr Kunz, Ayla Reynolds.
She wanted him publicly considered dead--so I think money was the motive--the Go Fund me and/or life insurance. Maybe to pay off drug debts--she was an admitted former user. Or maybe just for the money itself. I mean, if you can burn your baby alive, then you are callous enough to kill him for small cash. Sick.
Still, she is quite stupid. The more elaborate the plot, the more likely to get caught.