eBay's banned link policy will only affect sites that promote the sale of non-eBay items. Thus, Auctiva will not be affected.
On the other note, I am not too worried about Auctiva's templates. To my understanding, I would agree with nahoaloha and assume Auctiva just needs to tweak their templates a little bit. I just hope that saved listings will automatically be updated to any new changes made to the templates.
Jack