"a single human creature" refers not to 'he', but to the rest of humanity. I.e. "How could he ever know that anybody (even one single person) was on his side."

The protagonist is unsure if there is someone who is on his side. "to be on someone's side" means to be in support of the views of someone. The protagonist is uncertain that there is even a single person ("human creature") with the same views as himself. The question here is only rhetorical. The answer implied is "None." If the sentence structure is confusing for you, try replacing "a single human creature now living" with "someone": "What certainty had he that someone was on his side?" I hope it is more clear now.