Running bitcoin feels like its indexing my harddisk. [...] I don't mind the CPU usuage, but its seek behaviour is ridiculous.
Sounds like the problem I noticed, only with spinny disk instead of Compact Flash (cheapskate SSD drive).
https://www.bitcoin.org/smf/index.php?topic=274.msg23624#msg23624 (a sticky topic)
Did performance improve once you finished fetching the block chain?