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I don't understand why you need to fill in crushed rock or sand. Just build the wall and be done? the entire area would be below sea level but that's not unheard of: The lowest spot in the Netherlands being nearly 7 m below sea level.
Guessing you'd have to keep pumping anyway. A question is how long it would take for rain input to turn water bodies from salt- to freshwater.
PS Understandable but shame to have it as an April Fool's thing. Seems sensible to me. An instance of pushback against innovation starvation (Neal Stephenson's phrase).
Under the cost estimates we have in the article, it would be substantially cheaper to fill it in - cost of doing so is only 9% of the total cost, compared to 12% from merely having the pumps active for 100 days - of which half is the cost of the backflow during that length of time. We now think our backflow estimates were probably too high (especially as rain seems to be a substantial portion of the water ingress in similar projects), but it remains the case that it seems that managing to avoid pumping altogether after filling has begun would probably be cheaper on net.