If you are having sanitation problems with your bottling process, you need to solve that problem first. Kegging requires the same cleaning and sanitizing that bottling does. I would recommend addressing that before making a decision on how to package your beer.
While there are several techniques that are used successfully, I find that a thorough rinsing soon after emptying a bottle of beer is a good place to start. Once you accumulate a bunch of thoroughly rinsed bottles you should give them a good soak in PBW, or a similar product, followed by a close inspection and scrubbing as needed. Once they are squeaky clean and you're ready to fill them, sanitize with Starsan or Iodophor per manufacturer's instructions.
I would also suggest that if you have sanitization problems while packaging, you likely have them in other parts of your process as well. It has been stated many times in all of the popular How-To brewing books that the 3 most important steps in brewing great beer are sanitize, sanitize and sanitize. Neither of those 3 steps will do a bit of good unless everything is thoroughly cleaned first.
