Correct me if I'm wrong, but isn't holding your funds in paper wallets a sure way to protect yourself from hacks like this?
Good question. And the next one is: how safe is MyEtherWallet?
I seriously have questions about myetherwallet. If classic ether wallet can be compromised then myetherwallet has a chance too

Theres a very high possibility that Myetherwallet could get hacked sometime if the guys that manage that website want to hack the database. I know that many Ethereum wallet owners dont like to download the whole Blockchain for that coin so they choose to use Myetherwallet instead and they dont think about changing the password while doing it to secure their money.
Its pretty simple to change a password to secure a wallet, just have to do it.