How to safely ground a device plugged into an isolation transformer
Having the earth pin of the secondary plugs lessens the safety of the isolation transformer. 

The purpose of an isolation transformer is to float the secondary remove reference to earth. What this does, is that if any one connection is made to earth that connection will reference to earth and there will be no difference in potential. For example, if a person touches any one wire and something earthed. The difference in potential will be zero and the person would not get shocked. 

The earth pin connected to the chassis of the transformer which is in tern earthed degrades the safety. This is because if one of the secondary phases shorts to the earth pin (chassis), the one wire protection is lost. It is only safe to touch the phase that is shorted. If a person touches the other phase and something earthed they will get shocked. 

The drawback of the isolation transformer and not having the cassis earthed is that a fault to the chassis (earth pin) will go unnoticed. If a person touches the none shorted phase and the cassis of the unit they will get shocked. The workaround is to high pot or at the bare minimum to resistance check the earth pin to the other two prongs before working on the device.