>Checksumming only the file system's metadata and log, but not the user-level data, is a reasonable compromise
Within reason, my goal is to have a much confidence as possible in my data's safety, with as little investment of my time and attention. Leaving safety up to individual apps is a pretty wretched system for achieving this -- it defaults to "unsafe", then I have to manually figure out which stuff needs more guarantees, which I'll screw up, plus I have to worry about all the bugs that may exist in the eleventeen different checksumming systems being used in different codebases... This is the same reason I do whole disk backups instead of trying to pick and choose which files to save, or leaving backup functionality up to each individual app. (Not as crazy as an idea as it sounds -- that DVCS basically has its own backup system, for instance; but I'm not going around adding that functionality to my photo editor and word processor too.)
Obviously if checksumming ends up causing unacceptable slowdowns, then compromises have to be made. But I'm pretty skeptical; it's not like CRC (or even SHA-1) is expensive compared to disk access latency, and the Btrfs and ZFS folks seem to think usable full disk checksumming is possible.