When you want to sweep your private keys in Electrum it is like you send them in transaction,only difference is that you give Electrum option to send transaction for you from one or more private keys in single transaction.In this way your BTC will be send to a new generated address in Electrum but for that you need to pay fee.The difference you see in your blockchain wallet and final balance in Electrum is fee you need to pay for sweep.
You have option to continue with sweep,to send BTC direct from blockchain to your new address in Electrum(I think blockchain wallet allow manual fee)or you can import private keys in Electrum and not pay fee.But if you import private keys then they will not be included in your wallet protected by seed.For more info read Electrum FAQ : http://docs.electrum.org/en/latest/faq.html