I am unfamiliar with the type of algae that grows in hydrocarbon only environment. I am very familiar with the type that grows in a salt water and hydrocarbon environment because we deal with them in the oil field. Once we discover we have bacteria or algae growth, we flush everything in the flow loop with biocide (tanks, vessels, pumps, etc). In tough cases, we even have to have scale physically removed from the bottom of tanks so the biocide can reach all the algae hiding in the scale. It is tough stuff and once it gets a foothold, it hangs on.

This stuff that grows in diesel may not be as tenacious, but I am betting once you find it in your system, it is worth running biocide through everything.