An interseting concept. From my point of view, it would be more useful to have a three month rental term available. That's all the time a non-EU person can spend in the EU without jumping through the visa hoops.
Would sticking to outboard motors simplify things? I like the idea of keeping it "small boat" and simple. I would assume you'd have to outfit the boat with the basic safety gear, of course. Additional gear that a traveller would not necessarily bring with them could be offered for rent.
Another option would be to have someone purchase a boat and then donate it to the charity. The charity would provide the basic maintenance for the boat and would have it available for its use for nine months. The donor would be able to use the boat for three months of the year.
Stephan Knopf does something similar with motorcycles out of Heidelberg, Germany although his is a commercial operation. In addition to bike storage and rentals, he offers a comprehensive package of short term health and accident insurance, roadside assistance and emergency coverage, etc. He rents luggage, gps's, cell phones, and protective gear as well. www.knopftours.com