I don't see it that way, otherwise why does Alduin not call off the dragon's for the rest of the game, no, Alduin definitely wants the dragon born dead because he/she is a threat.
Perhaps to challenge Dragonborn, prove his worth...?
I'm kinda thinking it's similar to Morrowind where even though Dagoth Ur was responsible for a bunch of Ash Creatures attacking you, he still had a relatively peaceful conversation with you at the end. I wouldn't argue that the Dragonborn isn't a threat to dragons but that there's more to it than just kill all the dragons. I think it's either:
1. Dragons can absorb your soul like you can absorb theirs, so Alduin doesn't want the Imperials robbing them of it. As to why he spared you.. he was saving you for dessert.
2. Alduin needs you for something, more specifically he may need you juiced up on dragon souls, which is why he sends dragons to you.
3. Alduin came to kill you and got distracted.