What occurs to me relates to a discussion we were having here about the tidying-up lady whose book has become a sensation. As I recall, one of her maxims was, don't focus on what you want to get rid of, focus on what you want to keep. With that in mind, I would suggest making this decision not based on what you hate (basting), but based on what you enjoy. I think the two main questions to ask yourself are: Would I rather sit down or stand up while quilting? Would I find it more intuitive/enjoyable to move the needle over the quilt, or to move the quilt under the needle?
Best option -- try both methods and see which one you like better!