I will hold BioWare to their word about ending Commander Shepard’s story with Mass Effect 3, but they’d be crazy to not put out another game in the Mass Effect universe. It’s safe to say that Shepard’s actions in Mass Effect 3 will affect the fate of the universe in a big way, thus necessitating import saves for the next Mass Effect game, whatever it is.
So, for the time being, keep calm and carry on. Buy Mass Effect 3 when it comes out on March 6th, beat it on March 7th, and then keep the saves saves until further notice.
This won’t be a problem for me: I haven’t made a habit of deleting old saves since consoles started coming with hard drives.