Retrieval-Augmented Generation (RAG) is vulnerable to knowledge poisoning, where adversaries manipulate retrieved evidence to influence model outputs. Existing defenses are primarily evaluated using attack success rate (ASR), which obscures defense-induced failures and the mechanisms behind apparent attack prevention. To address this issue, this work introduces \textbf{Aligned RAG Evaluation}, a matched-query protocol that jointly examines clean and poisoned responses, with and without defense. By combining matched conditions analysis, LLM-judge endorsement, and retrieval dependence controls, the proposed framework distinguishes prevented from introduced failures, target mentions from LLM endorsement, and single-passage influence from evidence composition. Experiments on HotpotQA and Natural Questions reveal that existing defenses can introduce unexpected target-positive answers, although they can prevent some attacks, while evaluation criteria can also change defense rankings. Our findings expose critical blind spots in ASR-based evaluation and motivate a more comprehensive assessment of RAG poisoning defenses. The code and the evaluation artifact are available at https://github.com/chxhana/aligned-rag-eval.

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