Why was the 307’s pressurisation system removed when it was modified into the C-75, despite the fuel-burn advantage of higher-altitude flight?
Pressurization is primarily for crew and passenger comfort. The B307 was a very early attempt at cabin pressurization and the marginal pressurization differential of only 2.4 psi did not allow much of an increase in cruising altitude. 

The difference between 8,000’ and 12,000’ did not really justify the added expense and weight.

When the B307s were converted to C-75 military cargo configuration, there was even less justification for pressurization as military crew and passengers would not expect the comfort of pressurization. The C-75 could still fly at altitudes up to 23,000’ but the crew and passengers would just need to use supplemental oxygen. 

The B307 had Wright R-1820 engines which were similar to B-17 engines except they were only supercharged and lacked turbochargers. Cabin pressurization was supplied by compressors mechanically driven by the engine. These compressors would rob the engines of power so removing them would allow the aircraft to fly higher but with less comfort.