Harmful fine-tuning (HFT), performed directly on open-source LLMs or through Fine-tuning-as-a-Service, breaks safety alignment and poses significant threats. Existing methods aim to mitigate HFT risks by learning robust representation on alignment data or making harmful data unlearnable, but they treat each data sample equally, leaving data vulnerability patterns understudied. In this work, we reveal that certain subsets of alignment data are consistently more prone to forgetting during HFT across different fine-tuning tasks. Inspired by these findings, we propose Vulnerability-Aware Alignment (VAA), which estimates data vulnerability, partitions data into "vulnerable" and "invulnerable" groups, and encourages balanced learning using a group distributionally robust optimization (Group DRO) framework. Specifically, VAA learns an adversarial sampler that samples examples from the currently underperforming group and then applies group-dependent adversarial perturbations to the data during training, aiming to encourage a balanced learning process across groups. Experiments across four fine-tuning tasks demonstrate that VAA significantly reduces harmful scores while preserving downstream task performance, outperforming state-of-the-art baselines.