Graph-based Network Intrusion Detection Systems (GNIDS) have gained significant momentum in detecting sophisticated cyber-attacks, such as Advanced Persistent Threats (APTs), within and across organizational boundaries. Though achieving satisfying detection accuracy and demonstrating adaptability to ever-changing attacks and normal patterns, existing GNIDS predominantly assume a centralized data setting. However, flexible data collection is not always realistic or achievable due to increasing constraints from privacy regulations and operational limitations. We argue that the practical development of GNIDS requires accounting for distributed collection settings and we leverage Federated Learning (FL) as a viable paradigm to address this prominent challenge. We observe that naively applying FL to GNIDS is unlikely to be effective, due to issues like graph heterogeneity over clients and the diverse design choices taken by different GNIDS. We address these issues with a set of novel techniques tailored to the graph datasets, including reference graph synthesis, graph sketching and adaptive contribution scaling, eventually developing a new system Entente. By leveraging the domain knowledge, Entente can achieve effectiveness, scalability and robustness simultaneously. Empirical evaluation on the large-scale LANL, OpTC and Pivoting datasets shows that Entente outperforms the SOTA FL baselines. We also evaluate Entente under FL poisoning attacks tailored to the GNIDS setting, showing the robustness by bounding the attack success rate to low values. Overall, our study suggests a promising direction to build cross-silo GNIDS.