This is more of a system issue than bad behavior of an individual charity.
Charities can underpay a little bit, because working for a charity has its own appeal. But if you want a talented, experienced person to run your org, you have to consider what they could make if they worked for someone else. San Diego is not a cheap city, and has its fair share of CEO positions.
If you really want to stretch your dollar though, local food banks are probably a better bet.
tbf, bootstrapping a navy on the fly like that was probably a lot more doable back in the day. Galley warfare had a lot in common with ground warfare, and the Med is fairly forgiving waters.
If Napoleon had pulled it off vs Britain or something it'd have been infinitely more impressive.