HOOOOOO boy. That's a curveball. Obviously they use the blood collection room for genuine blood transfusions to help patients who have anemia and other shit. The only question now is not whether they collect blood, but whether someone's skimming off the top.
I doubt this will be about evidence gathering. The most likely explanation will be that they supply blood to other hospitals and it'll become apparent that Ciel is one of the customers who runs some bogus hospital in London or something. They'll have to choose between tearing down a facility that genuinely helps people or failing their mission.