Priming Non-toxic primer?

Technically, anything that can be easily sanded and doesn't react badly with the silicone and other materials can be used. You can use a sponge on method, just like some people do for face-ups, just be prepared to spend more time sanding that you would with a spray on primer, since the aplication is never as even. I don't know what your needs are or what materials you are working with, but if you need a lot of surface work (rought sculpts, filament prints etc.) a two step process with some sort of a filler first and primer after will make sanding a bit easier.
Check out what is available in your local paint stores, hardware stores and maybe even hobby stores.

Anything you spray on will require ventilation and the appropirate mask, even if the primer itself isn't toxic. It may still be an option if you have a well ventilated workshop/workroom, though. Additional tricks like spray boxes and such can also help. It doesn't magically make anything safe, but it does make clean up a lot easier.