Evaluating multi-paragraph clinical question answering (QA) systems is resource-intensive and challenging: accurate judgments require medical expertise and achieving consistent human judgments over multi-paragraph text is difficult. We introduce CQA-Eval, an evaluation framework and set of evaluation recommendations for limited-resource and high-expertise settings. Based on physician annotations of 300 real patient questions answered by physicians and LLMs, we compare coarse answer-level versus fine-grained sentence-level evaluation over the dimensions of correctness, relevance, and risk disclosure. We find that inter-annotator agreement (IAA) varies by dimension: fine-grained annotation improves agreement on correctness, coarse improves agreement on relevance, and judgments on communicates-risks remain inconsistent. Additionally, annotating only a small subset of sentences can provide reliability comparable to coarse annotations, reducing cost and effort.