The admonition against using the on board flash is stems from how flat and harsh that light is. If you have a speedlite, you can bounce it, diffuse, take it off camera, etc... all of which mitigate how flat and harsh the light is. With the on camera flash... you don't have any of that control.
In the scenario you were in, even if you had raised the ISO, you might still have trouble properly exposing his face. Not only is it dusk and getting darker, but he's also wearing a wide-brimmed hat that casts more shadow on the face AND the scene is very strongly back-lit. You were right to think that you needed some sort of fill.
As a snapshot, the on-camera flash works fine and you've done better here than the VAST majority of parents could dream of. As a portrait, off camera lighting is needed, even a simple reflector might have sufficed.
The slight orange cast to his skin is likely caused by the White Balance being slightly funky because of the different temperature of the on-board flash and the ambient light.
Good looking boy. EXCELLENT snapshot. Different lighting could have made for a GREAT portrait. Keep shooting!