I found Jeroens post about memory consumption:
The amount of memory that MyDefrag uses depends on things like the number of files and directories on the disk, the number of fragments, the length of directory and filenames, whether or not NTFS compression is used on the disk, which MyDefrag script you are using, and more. A rule of thumb is that MyDefrag uses about 500 bytes of memory per file on disk.
You seem to have "special" files if you need 2KB per file. Apart from running the 64 bit version, there is nothing you can do right now. You have to wait for Jeroen, what he thinks about a "light" version.