Is it worth migrating from WS1 to Intune if we have Microsoft 365 E3 available?

I believe it is a good first step, and I would say even a requirement, but in no way is it a comprehensive security solution, even for endpoints.   There are many things that need to be addressed for security. In addition to this, there is XDR, MDR, more comprehensive AV for endpoints & Servers that stop attacks, Threat Hunting, Mitigation, PEN Testing, Security Training for end users, Multi-Factor Authentication (Microsoft's MFA is good but only for Microsoft products), Patch Management for Endpoints, Servers and Cloud Workloads, Network Access Control, Firewalls for On-Premise and Cloud server workloads, Network Segmentation, Password Management, Data Backups (3-2-1-1 Rule) with Immutable Backups, Power Backups, Physical Security, Monitoring, NOC/SOC services, and working towards a Zero Trust architecture...   But there are no single-point solutions that will make you secure, so don't get complacent. And you can outspend your profits if you do everything. Just remember it's best to have a layered approach that works together and looks at everything from a security perspective and how it integrates with your overall security plans and objectives to help identify holes and possible mitigations. Healthcare must do Risk Assessments by law, but I recommend that all companies of all sizes do at least annual risk assessments since there is so such thing as being too small or inconspicuous to be hit with malware or have a cyber security attack since much of the delivery is automated and not just by the script-kiddies of years gone by... Nation States are actively engaging in cyber warfare daily, along with terrorists, and opportunists looking to make big money from you...

It depends on your company's infrastructure. Check with your cyber team whether you can sync your endpoints to Cloud using Azure AD as Azure Registered/ Azure Hybrid AD join/ Azure AD join, etc.        1. So, if the ask is only to enroll them in Intune to leverage defender/BitLocker services - go directly to Azure AD's join approach.        2. If you still want to manage patch management/mcm BitLocker but Defender via cloud, the approach should be Azure Hybrid AD join.         3. You can still use autopilot using both of these approaches.