If you don't mind my jumping in:
The difference is in the intent as well as the action. It is only ethically permissable to kill humans when the ones to be killed are a direct threat - and an immediate threat - to the life of other human beings. Even then, we shouldn't use more force than necessary and we should make every effort to restrict our violence to the one who is a threat.
In the case of Osama, I'm not sure it would be ethical to blow up a building that is known to be a full, occupied children's hospital to kill him. The action of knowingly killing all those children in order to get one man who is technically no threat at that moment and who might be caught by other means and with less danger to others is not something we ever want to condone. Similarly, it is wrong to kill embryos who are no danger to anyone else because someone else might benefit from the products of their deaths.
On the other hand, if the building is believed to be empty except for Bin Ladin, it might be permissable to blow him up, and the building with it, as long as best efforts to protect others were taken. If he were holding the button for a nuclear launch that couldn't be stopped any other way, it would also be permissable to urgently act to blow him up along with the building and its other occupants, in order to save many lives.
I imagine that you believe that Bin Ladin is always an immediate and real threat to many lives as long as he is alive.
My hypothetical condoning of the targeting of a children's hospital did include a terrorist figure who posed an immediate and grave threat...that the killing of innocents as an unintended consequence would be justifiable for serving the 'greater good.'
But my BF spun this around (devil that he is) to question me on how I could be against stem cell research if I could condone the sacrifice of innocents for the 'greater good' in matters of warfare.
When you say that the 'difference is in the intent'...isn't the intent of stem cell research, to the proponents, a noble cause?