I havn't played the map, but i have been watching its development. What it sounds like is that in the process of allowing one team to reach the enemy base fast and efficiently, you have made it fast and efficient for intel carriers to escape as well.
The main route should be faster but more dangerous whilst the secondary route has more obvious handicaps such as distance, height disadvantages, but stealth perks, and oppotunities to infultrate deeper into enemy territory.
Your route mechanics are mixed and interweeve. Your primary and secondary routes appear undefined due to the variaty of handicaps you have implemented per route. This ends up splitting teams, rather than splitting classes into their specific roles and complimenting their individual class mechanics.
Generally speaking in 24 player CTF you'll want 3 entrances, primary, secondary and tertairy. The primary will be your main entrance, quick to reach, but readily defencible, yet large enough in size to accomodate player flow.
Your secondary passes up speed for stealth (generally) taking longer to get into the action, and handicapped in height or smaller bottlenecks. 2fort's issue is that both the secondary and primary entrances bottle neck in the same room beyond either entrance (amongst other design flaws), meaning that either paths perks are largely negated since players have still to pass the source of enemy players (spawn rooms).
The tertairy is used (only) by classes with jump perks (scout, solly and demo (obviously)). Allowing players to flank and reach key points within the base (this usually occurs via the battlements).
Ignoring RED's base (Because i only modified BLU), move your base like this. This will have certain ramifications that should resolve existing issues:
You define your primary route as the bridge, meaning players are more likely to encounter each other here. Rather than splitting teams into several groups, diluting them across your map, you split classes, enhancing their mechanics.
The seconary route is less advantagious to take, and so becomes more of a tactical choice depending on class and player positions etc.
Interestingly the secondary now leads to your maps tertairy route. This is not necasserily a bad layout design.
OR: if you do not want to change your layout
that much, the obvious (if not cheap) solution would be to erect a fence or wall there. But it doesn't really do more than slow captures down through controlling player movement more linearly, than it would resolve the larger issue at hand (player dilution). Hence, the more in depth recommendation i have made.