I disagree with your first sentence. I do not think intelligence in small children is simply the product of learning/conditioning. It is a capacity with which they were born, and which they USED to learn.
I also disagree with your contention that intelligence cannot be tested objectively. I would say that no man-made test of intelligence will ever be perfect, of course. However, I think the tests we have now (WISC-IV [children], WAIS-III [by far the most commonly used], etc.), that measure intelligence as an ability are useful and objective.
To bring this back to the OP's topic, I also think it makes sense that various infections can affect intelligence. We've known for years that several neurological disorders (GB, for one) can occur after various infections. It makes logical sense that multiple infections during the growth and development of the neurological structures could impact one's intellect. With that said, I didn't read the study so I can't say if they controlled at all for confounding factors, and I'm sure there were many.