Yeah, you're stuck, sir.

FAA vs "The Locals" is always a fun one. (fun = challenging) Echo asking The Locals to bend their rules a bit. Although there might be some creative ways around it. Off the top of my head..
1) What's your real estate situation like? You might be able to divert the 2 year storm offline and detain it out of the flight path, and have a spillter box or diversion weir that only allows flows past the 2 year storm into your larger 100 year pond, which I presume stays in the flight path.
2) What sets the 2 year allowable discharge? Is it a pre/post regulation or a fixed rate per unit watershed area? If it's pre/post, can you reasonably make the case that your pre discharge is higher than you're currently assuming? For instance, if you're doing a redevelopment then your pre condition probably has runways already, which might set that allowable much higher and allow you to widen your 2 year control.
3) Can you detain the 2 year underground in pipes or an infiltration manifold and divert the 100 year to a surface pond?
4) Will "The Locals" give you storage credit for void space inside a stone / gravel matrix? You could conceivably over excavate your surface pond and backfill with gravel, assuming 40% voids, and hold whatever 2 year volume remains past 48 hours down in the gravel matrix. That would make the FAA happy (no surface ponding past the drawdown time) and still allow you to meet your allowable.
I've got a half dozen other ideas along this vein too, which are all out-of-the-boxers. Possibly pricier, but might meet both criteria. Shoot me an email if you want to talk more offline. I think if I were in your case, I'd start by asking The Locals to cut you some slack. If they don't, craft a design utilizing a combo of 3) and 4), price it, and then call a meeting with The Locals and The Owner that lays out the increased price of the new design and ask again, nicely. Then let The Owner talk to The Locals Boss if The Owner thinks the cost is worth the hassle.
my .02
Hydrology, Drainage Analysis, Flood Studies, and Complex Stormwater Litigation for Atlanta and the South East -