This isn't entirely true. There's a number of people on SDN who were on the interview trail and ran into programs that wouldn't interview them as DOs and seemed to have roughly equal success as MD applicants that had lower class ranks and USMLE scores 20-30 points lower. These were in traditionally "DO friendly" fields. It sounds like there's plenty of top flight programs in those specialties that were still willing to interview them, so it's not catastrophic (and as Winged Scapula said, getting into one of these elite programs is unlikely to be all that important for you anyway), but it is more difficult. More competitive, less friendly programs would have more doors closed to you, but for the time being, you can still apply to AOA programs that MDs cannot, and those programs will still likely favor DOs even after becoming accredited by the ACGME.
Some of my fourth year classmates were questioned about the quality of their clinical rotations, so some residency directors are concerned about it, but as they rotated at solid sites with both inpatient and outpatient experience, it seemed as though they were able to defend their education enough to satisfy their interviewers.
Regardless of what happens with ACGME accreditation and a combined match, plan on taking the COMLEX. It sucks, since it'll end up costing you about an extra $1000 to take an extra Step 1 & 2 exam and it's a waste of a few days, but that's a drop in the bucket compared to the cost of your medical education, and it's only a few extra days of studying to prepare for the OMM portion of these tests.