It is not likely that gender discrimination helps to keep female crime rates down by any serious amount. What is more likely is that the sex roles into which we are all socialized help to bring about the disparity in crime rates. It is likely that if men and women were raised and socialized in the same ways, their crime rates would be more similar.
Discrimination can only reduce female crime rates if somehow women are not allowed to join criminal organizations or if they are not convicted when caught committing crimes. Most crime is not committed by organizations so women could surely commit crimes if they wanted to. Prosecutors are not, in my opinion, likely to let women off simply because they are women. Therefore, actual discrimination is not likely to be causing disparities in crime rates.
However, differences in socialization probably do help to create disparities. Women are socialized to be much less aggressive than men. They are socialized to follow rules. This is likely to help cause them not to commit as many crimes as men do. If women were raised just as men are and if they got the same messages from society that men do, it is likely that the disparity between their crime rates and male crime rates would decrease (though I doubt it would disappear completely).