We propose a theoretical framework demonstrating that popular Large Language Model (LLM) alignment methods, including Reinforcement Learning from Human Feedback (RLHF) and alternatives, fundamentally function as divergence estimators between aligned (preferred or safe) and unaligned (less-preferred or harmful) distributions. This explains the separation phenomenon between safe and harmful prompts in the model hidden representation after alignment. Inspired by the theoretical results, we identify that some alignment methods are better than others in terms of separation and, introduce a new method, KLDO, and further demonstrate the implication of our theories. We advocate for compliance-refusal datasets over preference datasets to enhance safety alignment, supported by both theoretical reasoning and empirical evidence. Additionally, to quantify safety separation, we leverage a distance metric in the representation space and statistically validate its efficacy as a statistical significant indicator of LLM resilience against jailbreak attacks.