The wallet.dat contains the privatey keys to the addresses and syncing doesn't change the content of this file.
So you could just stuff this wallet.dat in cold storage and it would be fine (also securely delete the one on the windows-pc).
I don't know if some of the other local wallets are able to import wallet.dat files, would be very helpful in this case.
Also yes, you could do the syncing with an other wallet.dat file.
An other possibility would be importing the wallet.dat into blockchain.info and sending all Bitcoins to a paper wallet / cold storage address from there.
https://blockchain.info/wallet/import-walletThis still requires you to be online for a short time, so if you have malware on your PC that reacts instantly (aka Bitcoin specific malware like wallet-stealer) you might be screwed.