Fine-tuning Large Language Models (LLMs) with Low-Rank Adaptation (LoRA) enhances adaptability while reducing computational costs. However, fine-tuning can compromise safety alignment, even with benign data, increasing susceptibility to harmful outputs. Existing safety alignment methods struggle to capture complex parameter shifts, leading to suboptimal safety-utility trade-offs. To address this issue, we propose Safe Pruning LoRA (SPLoRA), a novel pruning-based approach that selectively removes LoRA layers that weaken safety alignment, improving safety while preserving performance. At its core, we introduce Empirical-DIEM (E-DIEM), a dimension-insensitive similarity metric that effectively detects safety misalignment in LoRA-adapted models. We conduct extensive experiments on LLMs fine-tuned with mixed of benign and malicious data, and purely benign datasets, evaluating SPLoRA across utility, safety, and reliability metrics. Results demonstrate that SPLoRA outperforms state-of-the-art safety alignment techniques, significantly reducing safety risks while maintaining or improving model performance and reliability. Additionally, SPLoRA reduces inference overhead, making it a scalable and efficient solution for deploying safer and more reliable LLMs. The code is available at https://github.com/AoShuang92/SPLoRA.