Absolutely certainly safe and simple sd card removal: shutdown the pandora (dont hibernate), remove card.
In other tips: If you just want the data written to the card and can use Terminal, say "sync" to flush changes to disk. You can also try unmounting the card (all partitions if multi-partition card) to see if it is safe to remove (sudo umount /media/<NAME>).
Also, dont remove cards while the pandora is hibernated.
I think our current flush timer is like 5s or less, so it should be safe to just close everything that uses the card, wait >5s (and until the card activity led no longer flashes) and remove the card.
If you still have problems with the card, it might be that the card filesystem is broken (unclean ejects?) or something else wrong with the card...
You can try chkdsk (or the graphical equivalent, or dosfsck on a linux pc) it on windows if it a FAT card.