That is how the real world works outside of academia. Spending time/money on grade replacement is a risk. This is simply a tabulation and how information is presented change. This is not a sudden change in requirements or change in rules. Another way to look at it, there used to be a way to hide your poor grades from DO schools, they corrected their algorithm so that you couldn't, ie it is more transparent.
Again, I'm not saying that it was a good policy to do what they did, after all, I can't see any benefits that they derived from this. But, other than a gut emotional response, I have a hard time seeing how it is an application service's moral obligation to save applicants time/money. If someone goes out of their way to cost them time/money, I can understand. But, every action/inaction by regulatory bodies, both government and private "screws over" part of the population and their best laid plans.
I also have a hard time seeing this impacting that many applicants. It will shift GPAs, but will it ultimately affect the outcome of applicant cycles? None of us know for sure, but I can't imagine it having a huge affect.