ALTHOUGH JOHN STUDIED HARDER THAN ANYONE, HE FAILED THE EXAM.
IN SPITE ___________
IN SPITE OF THE FACT THAT JOHN STUDIED HARDER THAN ANYONE, HE FAILED THE EXAM.
I think your transformed sentence is correct and I would also say:
In spite of studying harder than anyone, John failed the exam.
The second sentence, I think, it is also correct to say: