It doesn't necessarily take a complex organism to fight disease. Pretty much every organism, including unicellular ones such as bacteria, possesses some form of innate immunity against that organism's most common pathogens. Simpler organisms fight disease by simply reproducing faster than the disease can kill them.
As for the brain having some sort of monopoly on "organizing intelligent bahavior", that is a complex issue. I wouldn't say that the adaptive immune system necessarily possesses intelligence. It consists of many small and relatively simple components that interact to produce complex behavior. Realize that during somatic hypermutation, the immune system is not intelligently choosing which mutations to generate. It simply generates a random sample of all possible mutations and then sets up a simple selection process that produces a result that looks intelligent to us.
On the other hand, one could plausibly make a similar argument about the brain's intelligence being the product of the interaction of individual neurons. Many people believe that our brains are no less deterministic than a silicon-based computer. Complexity is complex.
Anyway, to give you another example, cancer cells are subject to greatly increased mutation rates, and mutations that result in faster growth or better recruitment of nutrient-supplying blood vessels (vascularization) will quickly become fixed in the tumor as the cells with that mutation overtake the growth of others. This also provides an example where selection at the cellular level is at conflict with selection at the organismal level. Within the tumor, selection favors faster-growing cancer cells, but these same cells are clearly the most detrimental to the organism as a whole.