Engine harness and alternator got burned

All that should be covered under warranty and yes you should nt drive it with a burnt harness. It will effect everything as it can burn the computer next

It can be a safety hazard but normally when stuff like this happens the NTHSA gets involved as well as the manufacturer and they work on the problem to get it fixed. Most manufactures do everything they can because recalls (if NHTSA calls them) do absolutely no good for the manufacturer and Toyota has been having more than their share right now. This would be a major fix because the part will be returned to Toyota and they engineers get involved to see WHY this happened. They will probably replace the whole harness underhood for that area as there are about 4harnesses there. Once your sis fixed I wouldn't worry about it to much as if there is a recall yours will be probably included and it wil be looked at again to make sure the proper fix was done. It may be aproblem that has just come to light. Having worked at a manufacture it seems everything they test a vehicle for is good and is done well but when ever the consumer gets a hold of it something else seems to happen as you can't predict everything that any certain driver will do to a vehicle. And I mean this as saying that you have done anything but drive it normally. Some things happen during driving that can't be tested for.