Using nice to set a lower priority for the program doesn't seem to make any difference, but using ionice, it's possible to have bitcoind do i/o operations with less priority.
This gives you the processid:
Example output:
Use the process-id, the second number to the left and set the priority for i/o operations.
This seems to do the job for me:
Check the man page for ionice to learn more about io-prioritization for programs.
But this makes the desktop usable (more responsive) again for me, while bitcoind can continue to synch the block-chain.
Hope this was useful for some.