That is very unfortunate... The 'rock' stamp looks like they got a hale storm just after the pour. It also looks like a sand collector, I would not be happy with it. Hopefully someone with knowledge of the overlay will chime in. It sounds like it might be better than a concrete surface but I would do a lot of homework on it. Ask your contractor for some references that were done several years ago you can look at and get the customers opinion. You do not want him doing it if he has done done many before this.
If you do find a know reason why this might not be as good as the decking you paid for then I would insist on a full removal and re-pour. Mistakes happen but it is "His" responsibility to make things right. You should not end up with inferior product or one you are not happy with because of his error. I think judge Judy would rule on your side..