Yea its a bit of a limitation with the module, only work around is to make fields which are conditional not required. I think a ticket on open.silverstripe.org to look into this but the whole validation / rules gets pretty complex really quickly!
Thanks for the reply. It looks like the form will have no required fields anymore.
Here's another solution let me know if this can work. Can I populate all the fields with a value? So for example the hidden required fields have a default value or something so even though they're hidden and not field in they'll still populate and validate therefore submitting the form.