What it needs is a set of big traffic lights at each end of the runway and at every crossing. When ATC gives take-off clearance the controller hits a big button that turns all the intersection lights red and then the one visible to the departing crew green. Then they either stay red until the controller hits the other button or, if you trust the automation, it could automatically turn off the red lights as the departing aircraft passes. It still doesn't account for someone running a red light but it might at least cause a pilot to query ATC if given an instruction to cross when the light is red.