If you are transferring "immediately" after receipt (say back to back blocks when no other transactions have occurred), then yeah it's going to be "obvious". If (when) more transactions are occurring, it won't be much of an issue. The thing that could make it obvious beyond that simple timing analysis is going to be whether the specific amount is obscured, not whether your output(s) have been used by someone else. Auto denomination works to thwart this, and the "attacker" should be left guessing.
You're going to NOT want to use Shapeshift for the return trip, unless you break it up into multiple pieces and (ideally) leave a bit left over OR you trust them with your privacy for some reason.