The three wires are three phase Alternating Current (AC).
You will need to have a three phase rectifier to convert the AC into DC.
You are still going to have a high and variable voltage, so you may need to get a voltage regulator to cut the power to your battery charging voltage.
Yes, that rectifier is way overkill but could be useful if you want to use the MP as the generator for a largish wind turbine or microhydro application.
6 Schottky blocking diodes used for solar panels should more than enough to cope with measly human power!
As for overcharging, I don't think there's much chance of the human getting accidentally "left on" overnight... however, I would definitely recommend an mppt controller to match the voltage of the motor to the battery.
If the motor doesn't spin fast enough to even reach the battery voltage, then nothing is going to get charged so a boost converter will be needed, and if more than the battery voltage, then either the battery will clamp the output voltage and it can be monitored, or use a buck converter to prevent any chance of overcharging.
There are loads of DC-DC converters on ebay and aliexpress to choose from - but really have to know the expected input and output voltage range desired.