Even a small advantage like 1% will quickly propagate in a population, because it's about advantage over 1,000s of generations.
That this disease defence CAN be turned on, means some people would have at some point had a genetic mutation to turn it on.
As the GP pointed out, therefore it must be a net negative from an evolutionary stand point.
I also suspect it would be calorific consumption, as someone else said, so it might be ok.
However, there are plausible other explanations. For example there are medical conditions that result from a too aggressive immune system and it could instead be reducing the chance of that occuring.