This optimisation is not implemented in the current version of Agda. Alternatives include increasing the size of the stack, or rewriting the recursion to be logarithmic in the exponent, not linear.
I have also been told that:
There is ongoing work to deeply change the Agda.TypeChecking.Reduce module (among others), which hopefully would have a positive impact on recursion over builtin naturals as well.
Ticket on the issue tracker.