We hypothesize that optimal system responses emerge from adaptive strategies grounded in causal and counterfactual knowledge. Counterfactual inference allows us to create hypothetical scenarios to examine the effects of alternative system responses. We enhance this process through causal discovery, which identifies the strategies informed by the underlying causal structure that govern system behaviors. Moreover, we consider the psychological constructs and unobservable noises that might be influencing user-system interactions as latent factors. We show that these factors can be effectively estimated. We employ causal discovery to identify strategy-level causal relationships among user and system utterances, guiding the generation of personalized counterfactual dialogues. We model the user utterance strategies as causal factors, enabling system strategies to be treated as counterfactual actions. Furthermore, we optimize policies for selecting system responses based on counterfactual data. Our results using a real-world dataset on social good demonstrate significant improvements in persuasive system outcomes, with increased cumulative rewards validating the efficacy of causal discovery in guiding personalized counterfactual inference and optimizing dialogue policies for a persuasive dialogue system.