Please read again Babur expedition to India, he is aim was to conquer not exterminate race of pashtuns. Many Afghans after being defeated used to come with grass in their mouths and beg for mercy. Yes he did build skulls with their dead bodies also but his aim was never to exterminate. Here are two exemples, in one he pardon them but in one build skulls of dead body.
''Next, he turned southwest, marched towards Thal (in Parachinar) taking the 'Hungu road for Bangash'. On the way, 'the Afghan's of Kohat' attacked but were put to sword. Babur writes: "The suppliants threw themselves on the ground and placing grass in their mouth, cried out, 'I am your cow'." (This custom is also mentioned by Charles Masson, the famous 19th century traveler in his 'Narrative of Various Journeys in Balochistan, Afghanistan and the Punjab,' while wandering through these areas in the reign of Ranjt Singh.)
From Hangu, Babur continued westward to Thal, a town on River Khurram (Khurram Agency) from where he traveled south-east along the river on a track called Gosfand-liyar (sheep road) as it was not a frequent riding road. The valley of Bannu (the town was not yet founded) was plundered and when
Shadi Khan, the tribal headman, surrendered to Babur with 'grass between his teeth', all prisoners were pardoned.''
Afghanland.com Afghanistan King Babur of Kabul