End-to-end autonomous driving systems excel in common scenarios but struggle with safety-critical long-tail cases. Vision-Language-Action (VLA) models are promising due to their strong reasoning capabilities. However, most VLA-based approaches rely on positive expert demonstrations, rarely exploiting negative samples, leading to insufficient understanding of risky behaviors and safety boundaries. To address this limitation, we propose SafeAlign-VLA, a unified negative-enhanced safe alignment framework that incorporates negative data into supervised learning and reinforcement learning. First, we develop a counterfactual safety pairing paradigm to generate structured safety labels and counterfactual positive trajectories from risky scenarios via counterfactual reasoning. Then, a two-stage training strategy is adopted: negative-enhanced supervised fine-tuning for failure feedback and trajectory correction, followed by anchor-based group relative policy optimization that uses positive and negative trajectories as contrastive anchors to steer sampling and penalize high-risk behaviors via group-relative advantages. Experiments on NAVSIM and DeepAccident validate the proposed framework. SafeAlign-VLA achieves 89.1 PDMS on the NAVSIM v1 testset, improving over the baseline without negative data by 1.3%. On DeepAccident, it reduces the collision rate to 3.36%, while achieving 84.2% language accuracy and 85.8% risk prediction accuracy. These results demonstrate the effectiveness of the proposed negative-enhanced safe alignment framework for safe and robust autonomous driving.