Question: When I activate BitLocker, I imagine that will make it impossible to read any files on my Windows partition from my Ubuntu installation. Is that correct? 

Any way to *not* encrypt certain directories so I can access them from Ubuntu?

Answer: 
Neither BitLocker or NTFS encrypted folders are supported under Linux. Only way (that I can think of) that you can have encrypted content accessible from both Windows and Linux is to use [TrueCrypt](http://www.truecrypt.org/).
Alternatively you might also try an encrypted EXT 3 filesystem that you can access from windows using FreeOTFE. I tried Truecrypt before, but especially in combination with SVN, which causes a lot of file accesses during an update, truecrypt was very slow.