USAID isn't clinical trials, it's treatment subsidies in foreign countries and studies on the administrative efficiency of foreign healthcare bureaucracies.
> Similarly, right now, actual research is being halted
Obviously if you reallocate funding from trial A to trial B, trial A loses its funding. Whether this is a net cost or benefit depends on how they compare with each other.
It also depends on how institutions respond. If Harvard is doing trials A and C and that funding moves to trials B and D somewhere else, and as a result trial A gets canceled but Harvard chooses to continue to fund trial C out of its endowment, you now have three trials going instead of two. Maybe that's better. I doubt they were doing that on purpose, but if that's the result, it isn't necessarily bad.