As of now, it is the default behavior for the sub-task to inherit the Fix Version/s field from the parent issue as we can see from here and the current workaround is to remove the project from the projects 'Enabled for GreenHopper' in the GreenHopper configuration. You should find it no longer inherits the parent fix version as mentioned by Shaun Clowes. Looking from a different perspective, is it possible to have an option to choose whether this can be optional or not?

Perhaps some sort of of checkbox in GreenHopper that says something like?

• Inherit Fix Version/s from Parent Issue for sub-task