The semantics of the question can molecules be changed into atoms is silly if not ludicrous. All things are composed of atoms, and all molecules are the result of the unification of particular atoms into any given substance.
Can molecules be reduced back into their basic atomic parts, then the answer is simply yes. I really think we as a society of educated individuals should watch the predicates we use to define our experience of the world, so as to have a more accurate and clear picture of what the true definitive meaning of the world we call reality truly is.
Take for instance the sentence:"People are so greedy and self centered"
If we break it sections we can begin to understand the way that words influence our experience. For example, who is the word "people" referring to? Certainly not all people are "greedy". Yet if you are the person stating this belief then you will find your internal representation of the world may be one of distrust and fear. I know that this specifically has nothing to do with the topic of debate, and at the same time it does. We are often left with the right understanding of a given situation when we analyze the words we use to define the way the experience is conveyed within our perceptions.
To believe that there is a valid and concrete difference between molecule and atoms is ludicrous, for all things are composed of one consistent and ineffable source or origin, energy. Energy does not change but rather forms into new representations of its former system of existence. A glass of water is heated until it evaporates, the "state" of the water molecule has changed into the apparent separation of the hydrogen and oxygen the water still exists only in a different form of its previous self. The whole of the universe works this way, and all things are composed of the energy that is one common and unchanged thing, the state in which energy may be represented may appear different, and then we have the right to be left with the conclusion that it has changed, which is only our verbalization through vocal representation of our internal understanding of the experience of energy, but this observation does not add or remove the presence of the very same energy.
I don't know maybe I am just perceiving it incorrectly?