An employee is only as autonomous as s/he feels s/he has complete control over her/his own schedule. Instead of bounding work by fixed time schedules (unless required by routinized work, which most management is not), follow the model of the professor. Allow a person to set their own schedule, and measure performances based on accomplishment, not time spent on task. This requires the organization to be substantially better than they currently are at a) defining tasks, b) measuring outcomes, and c) holding people accountable.
Smash your time clock. Build out position descriptions that identify the tasks that are associated with a particular role or person. Allow and trust that person to put in the correct amount of time to accomplish the tasks needed to make the whole organization successful. Where is the harm if one person accomplishes a solution to your companies' thorniest problem in the least amount of time? This will free up your workforce to spend the "right" amount of time working on the "right" problems, and I suspect you will find that your people will spend more time than you would imagine on the various projects you need to get done.