Keep in mind that AQ intermingled with Pashtuns like that; the Arabs weren't much less foreign to them than us.
AQ did not quarter themselves on villages - they mostly stayed up in their own camps or were invited guests of specific warlords, i.e. Jalaluddin Haqqani. Marriage alliances were contracted, but only after years of interaction.

Also, AQ are all Muslim. ISAF is mostly not. That makes a huge difference.

'Sexual relationships' isn't exactly the same as marriages.
Both would be verboten in Afghanistan. First, Muslim women cannot marry non-Muslim men in most conservative Muslim societies, which Afghanistan definitely is. Secondly, Afghan women, especially in the rural Pashtun belts, generally do not make sexual decisions independent of family considerations. I don't see Afghan elders pushing family alliances on American soldiers. Even if they were, I don't see the average American soldier or Marine welcoming such advances. Your average 20-year-old grunt wants unencumbered sex from hot American chicks he can put on his camera phone and show the squad, not marriage to rural Pashtun women in burqas.