I think it might be helpful to compare it to Fire Emblem, another series that recently was in a position of "put up decent numbers or you may never come back." 250K was set as the benchmark that Awakening had to sell for the series to ensure it kept getting games, and while I don't want to assume that the same applies across all series, I don't think a 2D Metroid would be significantly more expensive to develop, especially given that the story, powerups, basic enemy design, and general world layout are already provided due to it being a remake.
Additionally, if memory serves, Nintendo described the sales as "firm" in a previous sales report. Unfortunately it doesn't look like Samus Returns will be the big sales revolution that Awakening was for Fire Emblem, but SR's numbers aren't some kind of doomsday scenario.