How about this, applying the same logic as with a partitioned USB to this.

Using mybitcoin.com for day to day transactions and when there's enough coins sending that to your linux wallet address, and backing it up from there.
You have the security of a backed up wallet for significant amounts, and the day to day ease of use of an e-wallet.

It feels like I'm missing some fundamental point on how this logic fails, could this work?