Correcting exposure flickering in time-lapse footage "in post"
The flickering you are talking about comes because you have chosen a too narrow aperture. Normally you can completely eliminate the flickering by choosing a wider aperture than f/8.

The reason is simple: The lenses are no longer controlled by a physical aperture ring. Today it's the camera's job to set the aperture, and if you choose a f-number higher than 8, the aperture has to move a lot in a short amount of time. This leads to an accuracy of maximum 96 %, thus resulting in 100-96=4, 4 in each direction: 4*2=8 %. This means that each picture can be up to 8 % different in exposure. (This percentage is of course dependent upon how good your camera and lenses are.)

But as you already have your footage shot you need to fix it on your computer. There aren't many programs to do this, in fact I couldn't find any, but a good one is Photoshop CSX Extended. The Extended version can work with video, thus making you able to correct each frame individually. But this leads to a lot of job!

Luckily for you there has been made an action for Photoshop CSX Extended to automate this process. (Think of it like a plugin for After Effects.) Just load your video and apply the action, and it will fix your footage completely!

The action is a part of a big action bundle called iNovaFX which only comes with this eBook: http://www.gmbooks.com/product/CS5.html. On this page you can see it in action!

I hope this will solve your flickering video! Have a good day!