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Medical Visual Question Answering (Med-VQA) is a challenging task that requires a deep understanding of both medical images and textual questions. Although recent works leveraging Medical Vision-Language Pre-training (Med-VLP) have shown strong performance on the Med-VQA task, there is still no unified solution for modality alignment, and the issue of hard negatives remains under-explored. Additionally, commonly used knowledge fusion techniques for Med-VQA may introduce irrelevant information. In this work, we propose a framework to address these challenges through three key contributions: (1) a unified solution for heterogeneous modality alignments across multiple levels, modalities, views, and stages, leveraging methods such as contrastive learning and optimal transport theory; (2) a hard negative mining method that employs soft labels for multi-modality alignments and enforces the hard negative pair discrimination; and (3) a Gated Cross-Attention Module for Med-VQA that integrates the answer vocabulary as prior knowledge and select relevant information from it. Our framework outperforms the previous state-of-the-art on widely used Med-VQA datasets like RAD-VQA, SLAKE, PathVQA and VQA-2019. The code will be publicly available.