Minecraft – How to control a redstone lamp with command block

Redstone Lamps (unlike glowstone and pistons) act like opaque blocks, not transparent ones. Opaque blocks have two main differences from transparent ones:

1. They power adjacent opaque blocks when given "normal" power (like a redstone wire running into the block), and they power adjacent transparent blocks (including redstone wire and pistons) when given "hard" power (like a repeater running into the block or a torch underneath the block). They will not power any adjacent blocks when given "soft" power (like power from an adjacent redstone torch).
2. Redstone wire, redstone torches, and other objects that "attach" to blocks can be placed on redstone lamps.

This means that redstone lamps behave mostly like any other solid block in Minecraft when it comes to how they are powered, so you can power them many different ways:

That configuration on the left is powered by a redstone torch under the middle block, like so:

While having redstone lamps be opaque opens a great deal of possibilities, it also has the unfortunate downside of making it impossible (unless there's a method I'm not aware of) to turn on a single redstone lamp in a floor made out of lamps from below, so keep that in mind when building structures with them.

There are few ways to carry controllable power up a 1×1 shaft. As far as I know, the layout you describe in your question, with one modification, is the best that can be done for below-ground powering. Adding redstone on top of the solid block allows one more layer. (I have omitted the lamps in front in order to show the mechanism.)

Note the second torch below which accepts a control signal.

Here is one way to transition from a redstone wire to chained torches within a 3×3 base:

The key design principle is that each torch in the torch-and-block chain can move the signal horizontally one block, so by moving it off to the corner, we have room to direct the redstone wire into the first torch. Many other patterns are possible.