Absolutely not an issue. The last thing you want when developing a prototype piece of software for a 1 ton chunk of metal is another bit of software plugged in that you dont control or understand.
That's nonsense. The car had a human backup driver and human pedestrians, all not under the autonomous cars control.
An automatic emergency brake doesn't prevent a computer or human driver from braking when it wants to. If the autonomous system can't even avoid interaction with emergency brake, the prototype belongs in a lab, not on a public road.