I presume its a setting within windows that gets the system to check for a disk every 1 second so it knows when something is inserted. Unless there's somewhere to change this time period (which i doubt there is), the only way to stop the light blinking is, as you say, disable the device.
You could alternatively just disconnect the front panel connector for the HDD light. This would prevent blinking, and would mean you are not required to disable the device. Although not the perfect solution, it does solve the problem.