Evaluation of medical artificial intelligence (AI) agents remains predominantly answer-centric, assessing only the correctness of final outputs while overlooking the quality of intermediate reasoning. We propose MedTraj, a framework that treats reasoning trajectories as primary objects for modeling the progressive refinement of clinical evidence toward diagnostic decisions. A reasoning trajectory captures the state transitions among medical concepts---from clinical observations through evidential reasoning to a final conclusion---making the implicit reasoning chain of a medical agent explicit and inspectable. Each trajectory is scored across five quality dimensions: coherence, evidence support, hallucination, completeness, and traceability. Controlled error injection introduces targeted faults into otherwise correct trajectories to establish causal links between specific reasoning failures and measurable quality degradation. Step-level filtering based on marginal contribution identifies which individual reasoning steps drive or undermine reasoning trajectory quality. Quality-weighted reasoning trajectory context feeds these evaluations back into the model at inference time. Experiments across CareQA, PubMedQA, and CECMed demonstrate that reasoning trajectory context consistently improves reasoning coherence. For the severity assessment on the CECMed, quality-weighted reasoning trajectory context nearly doubles the correctness over the zero-shot baseline while cutting the hallucination ratio by 87%. Experiments show that 15.3% of reasoning steps carry most of the quality signal, and that extending chains beyond four steps yields diminishing returns.

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