by Your Speculative Reporter
unbound by mere facts (spit!)
premise: there was method in the madness (not intended as mitigation or exculpation or exoneration)
The villagers had previously made clear to the US Army that they hated the Taliban and wanted them out but the Taliban had (forcibly) married themselves into the village clan structures. The local unwritten laws of hospitality and clan relationships thus make it impossible for the villagers to truly turn against the Taliban.
So perhaps this soldier figured that if he eliminated the family relationships in those two villages (i.e., massacred them in their sleep), the Taliban would no longer have any hold over these villages under the laws of hospitality and clan membership even if the fighters were or were not home at the time of the massacre!
[the preceding scenario is entirely speculative but has a high chance of being proven true at a later date, check back here for exciting postscripts when we know more]