Is it permissible for a Muslim student to prepare a study in the field of food hygiene and safety for an institution that may benefit companies producing alcoholic beverages, knowing that his heart is not at ease with it?

It is not forbidden for you to conduct the study if it does not pertain to a forbidden company. If there is a part of it that relates to a company specializing in producing alcoholic beverages, then it is not permissible for you to do anything specifically associated with it. However, general studies that might be beneficial in both permissible and forbidden matters, and were not undertaken for the sake of the forbidden, are not problematic.