Ultimately, it's a personal choice whether to use abx or herbals.
I do know that a Lyme researcher - Eva Sapi - did a study and found that Banderol and Samento are just as effective as Doxycycline.
www.townsendletter.com/July2010/sapi0710.html Why is your Naturopath having you wait to start the natural treatments? That might answer your question.
Do be sure to use lots (at least 30,000 units) of probiotics every day while using any of these treatments to help avoid issues with Candida and other things.