I agree with you, unless it's explicitly stated what de refers to, it must be det. This is called a presenting construction, I wrote much longer about them here: https://www.duolingo.com/comment/9708920 – As a native speaker of Swedish, it's easy to forget that they really don't like using the It is construction for plural objects in English.
For me, as a mathematician, I would consider a theorem a proven thought while a theory is more of a framework. So a theory is one way of looking at the world where you can have both theorems, conjectures and other things inside that framework.
The theory in itself can't be wrong, but it can be a bad model of reality.
Anyways, I agree, it's a weird sentence.
A theory is still speculation, even when it has been tested in experiments, and the expression "just a theory" suggests that further testing could expose flaws in the theory: