I was unable to auto populate stack chart with csv data. I went with manually processing it and providing it in format that Highchart like which looks like below:

chartOptions = {
  chart:{
    type:"column"
  },
  categories:['A', 'B'], // I was passing list of group
  plotOptions: {
    column: {
      stacking:"normal"
    }
  },
  series: [{name:'a', data:[2,null]}, {name:'b', data:[3,0]...] 
}

This is the only solution as for now.