McColgan, whose daughter Eilish has run against Semenya, expressed sympathy but backed the 2-1 CAS verdict as a necessary ruling to protect the integrity of women's sport.
The Honda rider led from the first corner to chequered flag at the Jerez circuit, heading a Spanish one-two-three with Suzuki’s Alex Rins 1.654 seconds behind as runner-up and Maverick Vinales third for Yamaha.
Osaka has struggled since splitting with her coach Sascha Bajin in February while an abdominal injury forced her to withdraw in Stuttgart eight days ago.
The match was being played one day before the 70th anniversary of the Superga air disaster which killed 18 Torino players and officials, wiping out the most successful team in the club’s history.
The Court of Arbitration for Sport (CAS) ruled on Wednesday the regulations were necessary for athletes with differences in sexual development (DSDs) to ensure fair competition.