The hardware wallet will indeed protect your coins.

All the fake version of Electrum does is attempt to generate, sign, and broadcast a transaction which sends the entire contents of your wallet to the attacker's address. If you are using Electrum as an interface for a hardware wallet, then that transaction cannot be signed with you manually approving it on the hardware wallet. Provided you don't just blindly accept everything the wallet says and actually pay attention to what it is doing, then you can reject the transaction which will prevent it from being signed and broadcast.