My 2006 Skoda Octavia 2L tdi is noisy and I suspect the auxiliary belt tensioner, I've checked online and I've found out the alternator clutch if failing can knock out the tensioner. Can I SAFELY run the engine with the AUX belt REMOVED to eliminate the noise,and other than spining the alternator clutch is there any other check?

You will be ok to run the engine with the aux belt removed. I assume your not driving it, just running it to see if the noise goes away. The red charge light will stay on as the alternator wont be charging the battery. The alternator clutch pulley should rotate freely in one direction and spin the alternator in the other direction. There should be no play in the pulley which could suggest worn internals. Try spinning the idler pulley to see if this is causing the noise.