The Soekris kernel configs from flashdist are the best way to go. You do not need to remove the MFS option but I would add the FFS_SOFTUPDATES option. The MFS option is used for building a file system in virtual memory. It has nothing to do with compact flash cards. Those are still supported using FFS. I would leave MFS support in the kernel. You can find out more from mfs(8).
Bryan