While I don't remember how previous rehabs of the Rivers of America went, I don't THINK that's as much of a concern at this point. Fantasmic! is currently slated to come back for Memorial Day weekend, so I'd be fairly surprised if the refilling took too much longer than expected.
I can't say it's impossible, but I think it's a bit of a different situation. When they refilled the lagoon at DCA, the only main at stake was really "making the park look nicer." There weren't any attractions, nor any show, hinging on it being refilled in a timely manner. (Several look nicer with it, fair enough, but they can still run.)
Obviously for the Rivers of America, there ARE attractions AND a show that can't occur until it's filled, so I think it's more likely that they'll work harder to stay on schedule.