Hi,
Well, ideally, it would be great if your template could properly support bootstrap radios since they support bootstrap.
Otherwise, you can deactivate the bootstrap radios and use normal radios by editing the file "login" of the view "checkout" via the menu Display>Views and changing the line:
echo JHTML::_('hikaselect.radiolist', $values, 'data[register][registration_method]', ' onchange="displayRegistration(this)"', 'value', 'text', $defaultSelection, false, false, true );
to:
echo JHTML::_('select.radiolist', $values, 'data[register][registration_method]', ' onchange="displayRegistration(this)"', 'value', 'text', $defaultSelection, false, false, true );