As long as the forts exist, they will call for auxiliary recruits who will rush from the barracks on the other city side, to train at the academy. Once they enter the academy they will disappear, since they can not now move on the walled off fort because of the blockage. As each recruit enters the academy, it will be immediately replaced by a new recruit emerging from the barracks. This will create an endless stream of auxiliary recruits flowing from the barracks to the academy.

With no access to the fort, the recruits cannot fill it up but they will continue trying as they march in an endless throng to the military academy.
This throng of recruits traveling along several roads constitutes a large standing patrol or auxiliaries who will intercept and attack any
enemy forces who manage to penetrate your city. Each one killed in battle is replaced quickly by a new on emerging from the barracks.

Using this internal defense with no additional defense, I fought off three Samnite invasions with most of my city surviving intact, although significant damage was done, since the battles occurred inside the city. It is a good "last ditch" if external defenses fail.

Variation-Canalised Perennial Patrol
Wall the barracks side of the city off from the academy side, leaving only one single channel between them. This channel should run out of the barracks side, and back into the academy side, near the city entrance. (Similar to the Cobra defense but without the undulating road.)

The auxiliary patrol will move out of the barracks side, across this entry point, and back into the academy side, and will intercept all invaders trying to push into the entry point
[Terratheon]

Comments
This patrol of auxiliaries is not as effective as lions or gladiators, since you can use only relatively weak cavalry or javelin troops, who are poor at hand to hand combat.

The primary advantage is that the recruits move very quickly, are not restricted to a road, and will use several roads or other spaces when they patrol, not just the one or two roads used by gladiators or lions. Auxiliary coverage is therefore wider and more flexible. The javelin troops will often shoot at enemy invaders but for the most part will fight them hand to hand and don't do real well here.

I have generated as may as many as 53 barracks, with the barracks cheat, but the game freezes out often so I scaled down to 32 barracks which works fine.
How to create so many barracks? use the pause button each time you lay down one, and un-pause after you have repositioned to construct the next one.

CAUTIONS: This does not really work with heavy legions, whose number are limited by the quantity of weapons you have on hand. Don't form your auxiliaries emerging from the barracks into formation: Once they are called
to stop, they will stop moving to the academy and will no longer be replenished by endless replacements.

One further use, is to create more than 16 troops per fort: as the recruits flow toward the academy, their numbers will fluctuate wildly, and since thee barracks are producing all out, the auxiliary legions number will rise to 20, or even 23, as they flow toward the academy. When this occurs, click on any member of the legion and move it to a blank spot away from the academy.
Usually, 16 will form up and the extras will disappear into the academy, but if you break open the wall around the fort, and move the troops there, than most or all of the extra will often survive. However, they will go into the fort and won't come out to join the other 16 deployed outside.

I'll be experimenting with this more.
[Terratheon]

See also: Cobra defenses