Confusion over 'change' when transferring funds from bitstamp to paper wallet
You are correct, the rest of your funds will be diverted. However, they will be diverted to a new "change" address that is also managed by your wallet. So, you will still own the change.

For example, suppose your wallet contains 10 BTC [1]. If you send 0.01 BTC to a paper wallet address, then your client will automatically send the remaining 9.99 BTC to a new address inside your wallet. 

For more information, see the following questions:


Why do outputs need to be spent entirely?
Why does Bitcoin send the “change” to a different address?





This simplified explanation assumes that you originally had all 10 BTC sent to a single address. Normally, your wallet manages multiple addresses and adds up all the individual balances to show you the total wallet balance.