If you wish to allow Employees to work without this permission enabled for ClockShark to access locations "Always", you'll want to uncheck the box for "Enable GPSTrak location updates while clocked in via mobile". With that box unchecked ClockShark will no longer attempt to record GPSTrak location updates and will allow the Employee to use the ClockShark mobile app without the "Always" permission for ClockShark.
Here's what the "Enable" checkbox looks like in the Employees Screen in the ClockShark website.
The question when asked by the ClockShark app first looks like this: (Employees should choose "Allow")
Employees can access the setting at any time in their iOS Settings under Location: (Employees are required to select "Allow" if you have enabled GPSTrak for the Employee)