(1) He was much stronger [than he thought].
(2) You are much stronger [than I thought you were].
They are both fine. These are examples of comparative clauses. Comparative clauses are distinct in that they are usually obligatorily 'reduced' in some way when compared to main clauses. In (1), for example, the complement of "thought" is missing, but it's understood as something like "he was (strong)". The meaning is "He was x strong; he thought he was y strong; x > y".
And the meaning of (2) is "You are x strong; I thought you were y strong; x > y".