But the only reason they did that, is there are no user friendly ethereum wallets yet. Not sure whether it would be a good idea for Bitcoin.
Yes, that was only reason. Ethereum didn't have wallet and people were even losing funds because it was to difficult to install one.
What Kraken did is again different than what OP has suggested. People were uploading .json files. These are not private keys. That's like you upload your wallet.dat to the exchange. These files are also password protected while private keys are not. Therefore it's much more secure to upload these files than plain text private keys.