AACOM.org is a good source of information, both directly and as a reference to other sources. Maybe compare to AAMC.org. Clearly understanding the missions of allopathic and osteopathic medicine will help you decide where the source of the controversy lies, if indeed there is one.
It is true that MDs and DOs are equally capable, and that many MDs and DOs do exactly the same job, but this does not mean that allopathy and osteopathy are indistinguishable. Any applicant to an osteopathic medical school must have a clear and firm understanding of the principles at the heart of osteopathic medicine.
Many MD applicants (the majority of which are unaware of these principles) view osteopathic school as a back-up plan for those who weren't good enough to get into regular medical school. DO applicants for the most part, however, know what they are choosing, and choose osteopathy because it is osteopathy, not because of osteopathy's relationship to anything else.