During the scene where Morpheus is being interrogated, Agent Smith tells his colleagues to leave him with Morpheus. The other Agents seem very shocked by this move, and they almost reluctantly leave.
When Cypher is having dinner and the meeting up with Agent Smith, Agent Smith is totally by himself here for who knows how long. Why is it that it seems to be alright for him to be alone with Cypher in the restaurant, but when he's in what seems to be their own headquarters it's questionable?
Agents don't always work in groups of three. Sometimes they work in pairs or even alone. For example, Agent Thompson was the only Agent who appeared at the Burly Brawl (where the body he had possessed was assimilated by Smith). Another example is Agent Fine, who was the only Agent to appear in the comic "System Freeze".
Agent Smith met with Cypher by himself because additional Agents weren't necessary. The other Agents might have been busy with other tasks at the time, and possibly even working with one of the other Agents active in the Matrix (e.g. Agent Jones is seen working with Agent Finn in the comic "A Path Among Stones"). Also, it might look suspicious to the restaurant patrons to see multiple Agents (all dressed in identical suits) meeting with one other man. Multiple Agents would also be more conspicuous and make it more likely that Zion would detect the meeting.
On the other hand, it made no sense to the other Agents for Agent Smith to command them to leave during Morpheus' interrogation. That interrogation was the most important task for the Agents at the time (it would give them access to Zion's mainframe), so the other Agents didn't have a reason to work on some other task. Furthermore, the other Agents were already present, they were in a secure location (not a public place like a restaurant), and Zion already knew the Agents had Morpheus.
Actually, Jones and Brown do show up in a very brief shot during the restaurant scene, suggesting they were in fact helping Smith ensure the meeting with Cypher went well, if only as observers.
They're standing behind glass windows in what appears to be a darkened room just beyond the dining area, watching Smith speak with Cypher. The shot occurs directly after Cypher's "ignorance is bliss" line, when the harpist plucks at her strings. However, due to the speed at which the shot then cuts to a close-up on Smith, it's incredibly easy to miss.
- at :0:57 in the videoTo answer your question: Smith is conducting business as usual. He hasn't let his façade drop in Cypher's presence because Cypher has yet to prove himself useful regarding the obtaining of Zion's mainframe codes via Morpheus.
It's implied at the beginning of the movie that the Agents had to test Cypher's veracity before they would be willing to work with him. Agent Brown's line to Smith, "The informant is real," is confirmed by Smith's, "Yes." In this case, "the informant" would be Cypher, who had his call to Trinity bugged.
