Is the issue just large spiders? If you aren't seeing cockroaches or other disease-vectoring bugs, maybe you could make peace with the spiders and not use anything?
I always get wolf spiders in the fall, about 2-3 inches long. They eat all the other bugs, don't build webs, do their best to stay out of the sight of humans, and make great edible cat-toys.
Seriously, though, anything that will kill a spider will probably be harmful to your bees should they come in contact with it. There are non-toxic compounds like diatomaceous earth or borax, which will kill the insects your spiders would feed on (by desiccation) but may not kill the spiders themselves. These are also lethal to bees but if you spread them at the base of walls and inside windowsills the bees are unlikely to encounter them.