No Ulysses don't shot entire NCR or Legion.
He admits that missle can't kill NCR or Legion but can break their supply line so both NCR and Legion in Mojave will dry to die.
It's reasonable since NCR suffer from losing supply line(Divide) so cutting another supply line causes big loss of NCR.
That's what Ulysses learn from Courier.
You even played this DLC?
NCR:
http://www.youtube.com/watch?v=YB_LXgk-nkE - 0:04
"This will launch Ulysses' missiles against targets in the heartland of the NCR, raining nuclear fire down on it cities and its people."
As for Legion:
http://www.youtube.com/watch?v=dxLBSCZ1-xI - 0:23
"This will launch Ulysses' missiles against targets in the lands east of Coloardo controlled by Legion, raining nuclear fire down on its cities and tribes... (...)."
Please, play this DLC before posting something about it...
Because of people like you false informations are spreading, and then are repeated by others.