This minimap screnshot is what I am thinking. The black represents impassible marsh terrain i put the stargate grid (railroads) on. In this case, it shows the gate network going on the outside of the map with spokes to every planet. You can see that leaves a lane in the middle so ships can travel to all planets. Depending on how you look at it, this can also help with distance. For example, you can see the planets I labeled A and B. A represents a planet on the edge of the galaxy, and as such takes longer to travel to because a ship going from B to A has to move around the planets in the middle.
This leaves that red square in the middle open for space (sea) travel. The way i think of it, using this method you are just looking at the galaxy on its side instead of the traditional overview look. Ships can't use the gates this way, and in some cases the aircraft should be able to use the gate. From what I remember a glider can fit inside the gate wormhole.
As for the iris. I would make all the ends of the railroads the actual stargates, make an immobile unit called "Iris" that is placed on top of the desired stargate with a sizeable defense value to deter most intruders. Hence, your Gua'uld attack from space rather than walk into the SGC.
Just some thoughts, what do you think?