That's why you have to go with a microSD card adapter that doesn't protrude at all.
http://theniftyminidrive.com/
Are SD cards reliable enough for normal usage (excluding RPi's brutal power-off which are often prone to corruption) ?
http://www.raspberrypi.org/phpBB3/viewtopic.php?f=29&t=16289
Note that nilfs doesn't do checksumming -- for that you'd have to look at btrfs or zfs. I'm not sure how btrfs is in terms of ram usage, but generally zfs needs lots of ram -- and if you want to get the guarantees it provides for data, you need ecc ram.