Fortunately for Landry, both problems resolved themselves on their own when the two men broke through security and escaped the SGC through the stargate.
When the I.O.A.'s mission to reclaim Atlantis failed, Stevenson and Sheppard wanted to return the captured Tau'ri personnel through the stargate to Earth, but Landry refused, citing the security risk. Technically Atlantis and it's inhabitants had been deemed an enemy, even though they were former Tau'ri personnel, and Landry wasn't about to violate standard security protocol and lower the iris on the stargate, even to reclaim their own personnel.
Landry's decision proved to be in error, in that the iris was subsequently destroyed by Atlantis. No invasion or deception of any kind was forthcoming, just the return of personnel, as promised. A new iris had to be built to replace the scrapped one, and Landry found himself with a certain amount of 'egg' on his face. It was true that he had just been following protocol, but the decision by the I.O.A. to label Atlantis as renegade was truly at fault with Landry being caught between the two.
Later, when General O'Neill took direct command of the SGC in order to prevent the removal and relocation of the stargate, Landry was also caught between two conflicting sides. He was forces to ride the fence as long as possible without directly disobeying orders...problem was, he was receiving differing orders from his superiors. General O'Neill was his direct superior, but the President was the commander in chief and held ultimate authority.
O'Neill took the brunt of the responsibility on himself, shielding Landry and the other SGC personnel from responsibility, but once O'Neill fled Earth, Landry was forced to defer to the President's orders and allow the removal of the stargate.
Shortly after the removal of the stargate to an I.O.A. facility overseas, Stargate Command was shut down and Landry returned to his prior civilian life, preturbed by recent events but powerless to change the situation.