Does it clog on a single trip? If not, I would just clean the screen each trip, preferably after docking for the day. Consider it part of putting the boat to bed routine. If it clogs more frequently, maybe you could carry an extra screen and make a quick change while afloat but not under power. I suppose if you really had a severe problem you could plumb in a secondary filter with a quick-change valve, but that is a lot of complication to keep track of and another potential failure point.
The reason I say that is that the raw water contacts several hot areas and the greater mass of algae may "cook" there and clog things much more expensive than a screen, and present a much larger nuisance than cleaning more frequently. Heat exchanger, exhaust elbow, even a heater core if you have a heater installed would probably gain a coating.
That is speculation. But I am certain that the cooling effect of clean water is better than the cooling effect of algae-laden water, so even that might be a consideration to override the inconvenience of frequent cleaning.
Just my 2¢ but that is sure the way I would play it.
