@mschnell You can use industrial compact flash cards that don't have this low level integrity loss problem. As an example, we use the cards from STEC that are guaranteed not to become in an unusable state after a power loss. Of course they are a lot more expensive than the ones you can find in supermarkets ;)
@jpe1313 Could it help if you 'sync' often from the software, forcing a write on the compact flash more regularly? It could reduce the amount of work necessary to recover from the journal (and loose less data). I don't know if you can reduce the buffer size in the kernel to make that a bit more automatic...