If it is on a test stand close to the ground you are almost certainly seeing turbulence so it should be ok when you get it up into clean air.
Normally there is some lack of balance in the alternator itself and the final balancing would take care of that. It may be adequate to balance the blades alone if the alternator is very well made.
Adding weights to give a static balance is usually all that is required, when you can no longer determine a heavy spot it should be ok. It would be fine to check on a test stand before raising it to great heights, but unless you are pretty sure the wind is very modest it would still be wise to have the alternator operating and connected to a rectifier and temporary battery. At the very least have the alternator connected to a brake switch, then you can stop it if the wind picks up.
Now that you have explained what you are doing it seems a bit less frightening and turbulence is almost certainly causing your turning out of the wind. Bear in mind that things can run rough in turbulent conditions so don't confuse this with lack of balance.
If it is out of balance it will always be rough, but with turbulence it will only shake when the wind is swinging about.
Flux