Attention Toonami Fans, Rejoice!.

Considering the Major leaves her body, merges with the Puppetmaster and becomes a being based purely in the net, leaving Section 9 in doing so, I think it's a safe bet that the Ghost in the Shell films and the Stand Alone Complex series are of different continuities.

The events of Ghost in the Shell happen in the year 2030, the same year as season 1 of Stand Alone Complex in its continuity. The second season takes place about 2 years after season 1, with Solid State Society a further 2 later in 2034, by which point the Major has left Section 9 and Togusa has taken the role of Commander that the Major once held. She returns to Section 9 - still in her original body - during Solid State Society to help tackle the Puppetmaster case, the very same case that was the focus of the first film. The second film, Innocence, takes place 3 years after the original, with the Major left her body (which was destroyed at the climax of the first film) and Togusa showing no signs of promotion outside of now being Batou's partner, a role he took several times throughout both seasons of SAC. The films also make no recognition of several Section 9 members nor the Tachikomas, who appear throughout the SAC continuity.

You are completely correct about the style of the series though. The show does mark out episodes that are related to the season's story arc; and episodes that delve in to the Section 9 members or the current state of the world as "Complex" or "Stand Alone" respectively. They all happen in episode number order though, no Haruhi shenanigans here. The second season continues this, splitting them up further with stand alones and plot episodes that relate to one of two opposing factions. Can't quite recall what the titles of these were though.