Same reason the Gorosei didn't go after Luffy pre ts. Can't have the main protagonist and antagonist getting wiped out so soon (plus Oda didn't really think it through)
the government was trying to kill luffy since he first made himself known as a major threat in alabasta. its strongly implied rob lucci was specifically given orders to kill luffy.
in chapter 382 they already accomplished their mission and captured franky and robin, but Lucci holds them back and says "regardless of who is in charge of this unit, we're loyal to the world government" and when spandam asks him what he wants, he says "blood, when we're here, murder is justified."
later, in chapter 404, cp9 is being tailed by chimney and her cat. Spandam asks why Rob Lucci didn't eliminate them, and Lucci says that he only kills who he's been ordered to. Considering he tries to kill Luffy and targets him specifically in this arc, this strongly suggests Rob Lucci was ordered to kill Luffy.
also Kuma specifically offered to help Moria take down Luffy.
"If you think you might need my help, you need only ask." - Kuma.
"Are you telling me the Government is so scared they want to throw two of the seven Warlords at him?" - Moria.
"Before the incident at Enies Lobby, no one thought Rob Lucci could lose." - Kuma
so to me this means Rob Lucci was clearly ordered to kill Luffy, and so were Moria and Kuma.