Well you asked the question !
If it was just the thrust bearing it would make the noise when you press the clutch,not make it go quiet.The noise stops because the drag of the oil allows everything to stop rotating when the clutch is pressed.The noise is most likely a combination of worn bearings and gears.As long as it has plenty of clean oil in it and doesnt jump out of gears etc,carry on driving it.They were never very quiet - even when new,and can be very rough but go on for miles - but not without oil.(I say that because they like to do a bit of territory marking on owners drives)