Most likely the large amount of resources required to turn a Human into an Overwatch Elite makes it impractical. Plus, it wouldn't be good for gameplay.
Probably for the same reason the US military doesn't send Rangers, D-boys or other Special Ops and Elites in to every attack. It's redundant, and an unnecessary waste of elite soldiers and their hardware. Sending in multiple platoons of average soldiers is a much better way of dealing with one aggresive theoretical physicist and his rebels buddies.