yeah, you have to let them brake in, and there is a proper way to do it. hopefully they will cover it. maybe you should leave out the abuse part and tell them it was just fixed and there should be no reason for the engine light to be coming on.
Not certain you meant this but with new cars (I'd assume that goes for new engines too) you can drive them hard and it seals something better and gives you some benefit.. I don't know the facts but I searched online when I got my Celica brand new and I found out some good stuff.
But it's suggest you have some open space alone and run each gear pretty hard and then slow down relatively quickly and do this periodically for the first what ever miles.