When you shoot the flares, they "go out". The effect is achieved by a command block removing the flare.

More nicely built than on my screenshot you can see in this video (not by me):

If you hit the block on the wall behind the torch with an arrow, the torch is removed. So you can shoot out the torches.

Instructions:

The flares are removed when the block behind it on the wall is hit. The block becomes an "Arrow Block" by placing a [[Weighted Pressure Plate]] on it. This is because the pressure plate also notices arrows stuck in the block below it.

If an arrow is now in the block, the command is activated in the command block. As command one uses e.g. setblock ~2 ~ ~ air. The "~2 ~ ~" are the relative coordinates to the command block, so in this case it means the block that is 2 blocks further on the X axis.
Then you're done.

You can also make flares appear when you shoot at the spot. Or you can build a circuit that sets or removes a flare depending on the situation (see video).