Proper oscilloscope connection to prevent ground looping
Grounding loops are not your problem. The real problem is the unknown potential between the scope and the DUT. Without an Earth GND yes both are floating. (Does your scope even accept a 2 prong input without an Earth GND? Usually, most scopes have the chassis connected to Earth GND.)

If you just probe your DUT with the scope floating, you will attach the scope GND to the DUT GND, making that the common ground. The problem is that if the two are at a different potential then you are not protected from shock and may damage the equipment. 

Read this document by Tektronix. 

"The four safe solutions for these issues fall into four categories: battery-powered oscilloscopes, differential measurement systems, isolated-input oscilloscopes, and monolithic isolation amplifiers." source 

Alternatively, if you can guarantee the Vrms of your DUT signal you could do a differential measurement using 2 single ended probes by connecting their GNDs together and putting one on DUT GND and 1 on the signal. Then doing a math function on the Oscope to subtract the two.