We're not ruling it out, it's you that ruling out the scenarios that the circumstances and the few known facts are most likely--human intervention of some sort.
If lithium batteries did breach the pressure vessel at F350, the plane would NOT fly for seven hours after comms went out in a specific sequence.
I know all too much about the Stewart accident--batteries weren't the cause. You could look up the Helios accident for depressurization, too.
GF