That depends on what the reason for "not liking" the threads is. I'm aware of 3 considerations:
1) thread safety
... but that's always the case with threading
2) thread context and state
I have never run across an application container that does this by default though, typically that is only application logic which would dictate this. I can't speak to how WebSphere and current generation JEE containers do this as I have used nothing beyond a servlet container for several years.
3) module or application lifecycle
This is I believe the most common reason for the guidance. Launching threads within a container makes it easy to get a module or application in a state that it can not be gracefully shutdown and unloaded. Enterprise containers are often intended for dynamic deployment of one EAR/WAR module without restarting the entire container. Not being able to shut one down would prevent this or cause resource leaks.
If you call that in your Servlet destroy or application shutdown hook the EAR/WAR module should be able to cleanly shutdown.
I don't know if this fully answers the question but hopefully it helps.