Yes you can do it.
For this you need edit some (or all) masters in "Organization Chart Shapes" stencil.
1) Add new Custom properties to master and name it Color. Set Value for it 1.
2) Change FillForegnd cell value, to =Prop.Color.
3) In Wizard window, when it asking add custom properties, add this new Color in Data file columns.
Now they colored by value.
But value in Excel file must be number's. You see this numbers in Visio Pattern (Tools>Color pattern)