TNet is split into stand-alone and Unity side. Stand-alone is what's used by the server, and it doesn't use singletons / statics.
Unity side of it does use statics / singletons, and is because there shouldn't be more than one TNManager in the scene. TNManager.isPaused is used to put packet processing on hold while Unity is loading the scene. To decouple it, you could simply create a boolean flag on the GameServer that you could set, but at this point I would question the reasons for doing this in the first place. Why are you trying to remove the singletons?