A theory in science is a much more substantial thing than a theory in the vernacular. 'Theory' in the scientific sense does not imply any element of doubt; thus, we have the 'theory of universal gravitation', and the 'atomic theory', both of which are most certainly true.
Of course, a theory implies that a consensus of scientists accept it - in the science sense. However, as you are aware, many scientific theories accepted by a consensus of scientists at one time or another have been debunked over the years. Theories change, times change, and the search for ? goes on. What many Christian faithful (including many scientists) ask for is that creatinoism/darwinism not be taught as the truth - as proven fact because it is not! Teaching it that way, contricts the creative thinking processes of budding scientists.
After all, asserting that amino acids can be changed to DNA because of natural selection or fluxes in physical energy, or that reptiles morph into birds, or humans into apes makes no sense and cannot really be justified scientifically.