I faced the same issue and found a solution that works. I now have a system encrypted Windows partition, an encrypted data partition and a Mac partition, running Windows 7 and Mac OS X. See my solution here.
EDIT:
I realized, after reading negative feedback, that posting a link sucks, especially because my old article was gone. It was in an old blog that I don't have anymore, but I managed to salvage the article text from an old backup of the blog's XML storage. Here is the article in full length. Bear in mind that this is from 2010 and you are doing this on your own risk:
This describes the steps needed to be able to have a dual boot system with Windows 7 and Mac OS X and where the Windows partition is encrypted with Truecrypt. This is not done using Bootcamp.
Tip: If you are new on Mac, and you can't figure out why the machine does not boot from the Mac OS or Windows installation DVD despite you have inserted the disc, you can hold down the option key during boot (the one with the text alt). This will present you with a menu where you can select which OS to boot and if you wait a little while, the installation DVD will appear on that menu too. This is also what you use, when you select which partition to boot from later.
WARNING: The following steps will DELETE ALL DATA ON YOUR DISK. Okay, here we go:
Boot and insert the Mac OS installer disk and let it run until you can use Disk Utility to create partitions. Enter the Partition tab in Disk Utility.
Create two partitions: The first one on the disk is for Windows and the second one is for Mac OS. Format the first one as FAT32 and the second one as Mac OS Extented (journaled). We will reformat the FAT32 to NTFS during the Windows installation. Windows must be first on the drive for TrueCrypt to be able to encrypt it as a system drive.
In Options, select GUID Partition Table. This is very important. Apply the changes and make sure the information at the bottom of Disk Utility says that it is GUID Parttion Table. When done, close Disk Utility.
Install Mac OS on the partition you created for it. Let the installer complete.
Boot the machine from the Windows DVD, delete the first 200MB GPT Protective Partition (Mac OS will boot without it), delete the windows partition and create a new NTFS partition that fills up the beginning of the drive and complete the Windows installation.
Boot into Windows and encrypt the Windows system partition. DO NOT ENCRYPT THE MAC PARTITION. This also means that you may NOT encrypt the entire disk. Truecrypt will ask you all sorts of questions.
In Windows, insert the Mac OS X install disk and install the bootcamp drivers.
From now on when you boot, you hold down the option key to select between Windows and Mac OS. In Mac you can set which partition to start up by default. This can also be set in the bootcamp control panel in Windows.
You are done!
Note: During creation of partitions, I also created a FAT32 data partition in between the Windows partition and the Mac OS partition. I reformatted and encrypted that data partition with Truecrypt and both Windows and Mac have access to it. Nice!