That's because they had another ending planned, but scrapped it.
Shepard was supposed to make a totally different decision, after finding out that the Reapers were giant supercomputers that were trying to stop Dark Engery from engulfing the universe...and human DNA held the key for solving it (hence that bit about Mordin talking about human bodies on Tuchanka). In the end, Shep has to make a choice - kill the Reapers and let the galaxy figure out how to stop Dark Energy (which is close to critical) or do the horrible thing and sacrifice humanity to help crunch the numbers.
But they scrapped that because Dark Energy took the spotlight away from the Reapers, the player couldn't fight mathematics, and the whole magic human DNA thing was really just a stretch.
I don't know the full details, but that was where the plot was heading before.















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