I'd think a charge controller could be built using plain old analog methods with long feedback cycles that would avoid the hunting problem, though some battery chargers do use short pulses to float the fully charged batteries.
Where I see microcontrolers would be most useful with small wind turbines is for monitoring performance especialy when designing and testing them or for everyday logging.
The area of (commercial) windturbines I worked with was mostly in the control and converter/inverter systems. There are 4 seperate microprocessor based controlers on the z750s, but what struck me was that all the emergency and failsafe systems are mechanical or simple analog systems.
I've been doing some initial design work and overall "project" planning. From speed control and power conversion/battery charging to overspeed furling/pitching and I plan on using either mechanical systems or analog electronics (with the exception of things like TTL clocks)
I'd be very reluctant to put a microcontroler on a turbine uptower. Static can build up on a clear, calm days. One of the guys I worked with last summer got nailed by static on a clear day bad enough that his arm was numb for days.
A rule of thumb I'd use is, if it needs to be handled with an anti static mat and wrist strap it should not be put on a turbine. I'd make an exception for power MOSFETs with built in protection and a good circuit board layout.