We recently had, what I thought, was a very good discussion on 'Stall' here. You might want to look it over, because there are many aspects to it.  
'Stall' is not quite like 'braking'.  It usually is more like, 'It can't get going fast enough!'
What happens is, the mill starts up in 'free-spin'. (no load)  This is normal. As it spins alittle faster, the voltage keeps going up until it reaches the battery voltage (called:'cut-in').  Now the mill is no longer in 'free spin'.

 The battery starts accepting the current (amps) into it, at, and after this point.(battery voltage)  This is when the mill STARTS having a LOAD on it. (the "Load" IS the current that is now starting to flow into the battery, even though it starts out as a small amount of current, and increases as the mill turns faster and faster)

So one meaning of the term "Stall" is when the blades, in the lower winds, can't turn fast enough because the mill reaches battery voltage (cut-in) TOO EARLY, begins accepting the current/Load, and the mill simply gets 'stuck' at that low rpm because it can't reach a strong enough enertia momentum rotation.  Inotherwords, it can't get going fast enough rpm before the LOAD starts on it!

Lets say for example that you use your mill there with a 12v battery. You said you get about 50 volts per phase by just spinning with your hand.

When you bridge rectify each phase and hook the outputs together, it will be the same voltage as that, but with more amps capability.  The blades will reach 12v cut-in very fast(Too soon), probably around 30rpm or so, and then the battery begins accepting the current and a LOAD is now on the mill.  The blades will not be turning fast enough to reach "lift", nor a decent inertia momentum (rpm) to get over this initial LOAD. It will get 'stuck' at or around 30rpm.  

Looks like with that set-up, you really need a 48v battery bank , so the blades can spin upto a faster rpm before battery voltage 'cut-in'. (just guessing:say 120rpm for a 10 footer??)   I have no idea how your 'variable pitch hub/blades' will affect this. Should be interesting though.

"So is it the job of the charge controller not to start chargin the bank until a certain voltage is detected."

No. The battery does this on its own. The mill is in 'free spin' (no current is flowing into the batts) until the mill reaches the battery voltage, and then, and only then, will it begin accepting the current(load) and thus, charging the battery(S).

Charge controller keeps the batteries from over-charging and ruining by 'bleeding off' the 'extra' power after the batteries reach full charge.

Also, that is normally what happens when you short one phase- it is hard to turn. It should also vibrate badly. When you short all phases together, it is even more mega difficult to turn, but there should be no vibration.