Don't know about the antibiotics, but the laser is not for the castration, but the incision (I'm assuming) which just means that instead of a blade he'll be cutting with the laser vs. a scalpel. This reduces bleeding, pain, etc s it instantly cauterizes the incision.
Here's an ok website I googled real quick on it. As for removing stuff from the cage, consult your vet, but I don't know that anything but the litterbox need to be taken out. maybe the toys, to restrict movement. The litterbox concern would be that he has to jump in and the litter might get in the incision site and/or keep him in close proximity to urine/feces. Probably that need only be for a couple days, but again, check with your vet to be sure.
And when your vet says that antibiotics are 'toxic' perhaps he means that they can kill gut flora needed in digestion? That can lead to gut stasis, malnutrition, etc. For a routine neuter there really isn't a reason he would need antibiotics that I can think of. It's a sterile prep and all. If you trust your rescue, then I would stick with the vet. He does enough of these things to at the very least know what to do about common complications (it sounds like).
One thing- though, can your male touch your females? Animals can (and do) mate through fences, so be careful with that.