but i don't know why you complicate with linux and flash drives if a simple wallet with encryption and an offline btc client will do the job.
there are many secure way on how to store your wallet and btc you just need to find the right one for you.
If your machine gets infected with malware, your bitcoins might still get stolen. Even with encrypted wallets (at some point you'll have to enter the password, and any malware with a keylogger will sniff it).
The chance of getting infected is much, much larger on your everyday Mac or Windows system, than on a separate, dedicated (i.e. for Bitcoin-usage only) Linux system.
The stuff with flash drives is mostly for backup (in case your hdd crashes, your PC gets stolen, your house burns down or whatever). This issue can be resolved in other ways too, e.g. automated backups to remote locations, or even something simple like Dropbox.