You are right that there are some advantages with a Windows Service, but the biggest disadvantage is that it won't work for people using a hosting service. It would also require an installation program and a UI to interact with it.

GSP ships with the timeout increased to 24 hours, which should be enough for most people (change the executionTimeout setting in web.config if you want something different). In my experience, the most fragile aspect of syncs is the client-side ajax communication with the server failing. When this happens, the browser loses the ability to tell you how the sync is progressing, but it is still buzzing along on the server. That is annoying but at least the sync continues.

That said, I have no objection to someone creating a service and posting it here.