Why did Gus slit V-----'s throat?
For a number of reasons:1) Victor was spotted at Gale's crime scene and being the cautious man that Gus was he couldn't risk Victor being picked up by the police.2) Victor was cooking meth without permission and that angered Gus, as Walt said in Season 5 Victor "flew too close to the sun."3) Victor failed to save Gale's life. After the death of Max, Gale more than likely became Gus's new lover and therefore Gus took it very personally when Gale was killed.4) To scare the hell out of Walt and Jesse.
WalterThis is shown by the last scene of Season 4, Walt is sitting in his garden which contains a Lily of the Valley plant. It is later explained, in Season 5, that Walt used Saul and Huell to lift the ricin cigarette from Jesse, so Walt could convince Jesse that Gus poisoned Brock. This is why Jesse turns on Walt in the final season.
Did Walt violate the code of 'Omerta' in the Pilot?
No. The code of 'Omerta' prevents anyone who willingly enters organized crime from talking to the authorities no matter what happens to them or their families. In the Pilot Walt threatens to turn Jesse in to the DEA if Jesse doesn't agree to help him distribute meth but since Walt hadn't officially entered the meth business the code did not apply to him.Jesse on the other hand did violate the code in the "Rabid Dog" episode when he spilled his guts to Hank about Walt.