Police have control over vehicles now primarily to stop the behaviour of drivers who are breaking motor vehicle laws.
I agree, but Google is moving towards self-driving cars that don't have steering wheels. One day they may remove the brake petal. In such a case the car itself will have to be able to respond to requests by the police to stop. Similar issues could arise if one day we get the hyperloop.
If a police officer sees a crime such as murder or rape being committed in a self-driving car, they have every right to stop the car without the occupants permission.
I can't think of a valid reason an individual LEO should be allowed control of an individual self-driving vehicle, ever.
That happens today if the police are in hot pursuit. They take control of the car by doing things such as putting out spikes to blow the tires. There's been talk of EMP-like devices to blow out the electronics that every modern car uses. The legal justifications for this are well-established.