Starting from Secure Fields 3.0 we give an option to delete a Secure Field history and to not store it at all for the future.
So for instance, when you have a personal information and you are asked to not keep it any longer, you can simply delete the field value and whole history of it.
Also, if for some reason you do want to not store history of a Secure Fields at all, you can set it up, by going to:
Issues → Fields → Custom fields
picking the cog wheel by the Secure Field you do not want, then pressing
Configure → Edit Permission scheme → unchecking the box Save field history and clicking Done.
And there you go, history for this field will not be kept any longer.