This has also concerned me as well (and lots of others), and on Reddit we had some thoughtful discussion here:

http://www.reddit.com/r/Bitcoin/comments/hid2r/how_will_you_...

One of the best suggestions in there is simply to separate your checking and savings accounts so that a compromise of your spending money doesn't leave you without any coins.

There's also a link in there that says the upcoming clients will store the wallet locally encrypted and only decrypt in memory for transactions-- there are weaknesses to this (i.e. the bitcoin client trojan you mention), but it's better than what is done today to secure the file on disk.