Your interpretation would be correct if the sentence had said "think" instead of "suppose". However, "suppose" changes the meaning. A supposition is a special kind of thought. A supposition is a thought based on speculation, surmise, or guesswork.
My interpretation of your sentence is this:
"On the basis of the little he could remember of her, he could only speculate how intelligent she might have been. The few clues available from his memory were not enough to suggest that she was, in fact, unusual or intelligent."
Actually, she might have been very intelligent. He doesn't suspect that to be so, but he's not ruling it out either.