If it's true that these indirect costs only contain expenses closely related to the actual research then they can just move to the actual grant with somewhat more accounting overhead. I suspect the universities are doing that accounting already for their internal purposes so it won't be that big a change.
But if it's true that a significant part of them are not related there would need to be significant changes in budgets, and whoever benefits will have a problem.
I suspect the truth is somewhere inbetween. In any case it's a good opportunity for these organizations to figure out how to become more cost effective.