I have an ISA One with the digital card....and what you want to do is possible.
Here is an excerpt from the manual regarding the Insert / return:
Activating the INSERT switch (illuminated when active) breaks the signal path of the channel, so that the signal sent to the first ADC Input and the analogue output on the rear panel is the signal received at the INSERT RETURN connector (on the rear panel) rather than the direct mic, line or instrument signal. This switch is designed to allow the input signal to be routed to other hardware for processing and then back into the ISA One for digital conversion. The POST INSERT switch on the front panel allows the ‘return’ signal level to be viewed on the left-hand LED peak meter before conversion (see the Metering section on the next page for details).
Soo.....from the paragraph above it indicates the signal sent to one ADC input is the signal received from the 'return' jack...logically this would be post-transformer since the signal would already be amplified in a normal send/return scenario.
This would suggest if you put one channel in the EXT I/P, and one channel in the 'return' jack with the signal set to 'line' and the 'insert' button pushed you would get two-channel conversion without the transformer in the path.
NOTE: I just tested this with program material I am familiar with and and the answer is "YES" it works as described above. In this mode...the gain settings on the front panel have no effect on the signal...nor does the filter or the phase switch.
EXT I/P is the left channel. SEND RETURN is the right.
This mode basically turns the ISA One into a straight two-channel converter.
BTW there is a video on YouTube of a guy in a studio using the ISA One as conversion...
Hope this helps.