Shouldn't it be up to the teacher to point out when things they are learning are theory and not a proven fact?
But I do agree that the uninformed often don't catch on that it is a theory. Maybe it would solve a lot of problems if we started always calling it the "theory of evolution" just like one almost always hears the "theory of relativity" and not just relativity when referring to that theory.
I wonder what would happen to the hapless student who chose as a class project to do a term paper on the weaknesses and gaps in the theory of evolution? Would the ACLU come in and demand that his paper be given a failing grade because it contradicts the dominant paradigm? Maybe they'd demand that the student be sent to a "re-education camp" to purge him of his dangerous anti-social way of thinking.