+1 on the wine thief and not watering down your brew. Usually folks will use a 6 gallon or larger vessel for their primary so there's room for krausen, and then a 5 gallon secondary so they can fill it to the top with little or no headspace. Other folks just skip the secondary and leave it in the primary until it clears and bottle from there.
Let it be. As pkeeler said there is usually enough CO2 brought out of solution to stave off oxidation. Sounds like you just didn't quite hit your volume in primary or you left quite a bit behind. How long was your primary?
It was in my primary for 6 days. I'm brewing a dark ale from a kit. The instructions said to fill the primary to 5.25 gallons, so that's what I did. I didn't have much trub in the bucket. Only about half an inch.