St. Thomas' Classification Error

St. Thomas Aquinas used proto-scientific Aristotelian methodology to explain the Eucharist, and in doing so he unintentionally opened the door to various Christians ceasing to believe as Christians traditionally did. St. Thomas took a way of explaining the natural, or created order, and used it to explain something that is of the uncreated order. Now, obviously, there are people who believe that there is no uncreated order, and of course, they wouldn't believe in the Eucharist either. It is, however, extremely odd to find Christians who believe in some parts of the uncreated order and not others- and in this case, I think St. Thomas likely did more harm than good. The Eucharist essentially becomes captured in the West, as these arguments are integrated into the Christian gestalt, by the assumption that this is a created thing to which the scientific method can be applied.