Alll of the important Linux systems I've built have been scripted. Thus, I can re-image a host which I have any concern about in a matter of minutes, and I often keep checksums of every file on a virgin system. On BSD systems I can and have re-build world on just an unexplained re-boot just in case. And none of my systems are even sensitive enough to hold passwords, much less financial data. I don't even consider myself a competent system administrator!
The skill level demonstrated by most Bitcoin related 'businesses' is simply appalling to me, particularly since there is a financial component. No wonder fucking near every one of them has been hacked.
Hey want to do a bitcoin start-up with me? .... You sound like just the guy I'm looking for.
Hire somebody from openbsd-dev or henning brauer for consulting, the guy who maintains pf. He runs http://www.bsws.de/ and offers managed servers. Run the cold wallet yourself. Or look into google app engine and trust google's infrastructure