Sorry for not getting back to you more quickly, as I've been quite busy with rl stuff this week. The choke point I'm referring to is this (as far as I can tell this one doorway is the only route to the intel):
The added path I was referring to would be to open up the boiler rooms (or whatever they are) and have a way of getting directly into the intel room from there:
Although, now that you mention the scout rush concern that would definitely be a problem...plus the issue of having too big a playing field. After no-clipping around I see the "lower decks" that you are referring too. A good bet I think would be to reopen them, but leave the barricades there just make them destructible (like in cp_warpath if you've ever played that). This would prevent an early rush on the intel, while at the same time opening up an extra path after a Demoman or Soldier expends a short amount of time destroying them.
Of course I could just be talking out of my ass as I've never play tested this on a full server. Which, I will do now just to see how it works as-is. I'll be putting it up this Sunday night on the FearedGamers server (s1.fghost.org) if you would like to see it with 32 players. We do our own testing every Sunday at 8pm central time. No set times for each map though like they do here, so I wouldn't know exactly when it would come up.