While LLM-based Multi-Agent Systems (MAS) demonstrate remarkable problem-solving capabilities, their interconnectivity acts as a conduit for the rapid spread of malicious injections. Addressing the limitations of static defenses, we present TopoSHIELD, a framework that reshapes the flow of malice via risk-aware topological evolution. Our approach utilizes a spatio-temporal graph neural network to monitor interaction dynamics, calculating node risk entropy (NRE) and edge attack conductivity (EAC) to pinpoint vulnerabilities. Guided by these metrics, TopoSHIELD executes precise structural interventions, pruning high-risk edges and isolating compromised communities to block attack diffusion. Empirically, TopoSHIELD reduces toxicity by 58% on GPT-4o while preserving high utility (>90% success rate), outperforming existing baselines in both suppression efficiency and scalability.