I don't think the TGVs will allow bikes without being covered in some way, either in a box or with a bag ("housse"). Although, info I just saw on the excellent resource site
http://www.mayq.com/Best_european_tr...kes.htm#France says some TGVs on certain lines now have bike compartments.
I would suggest spending the extra euros for first class on the TGV. You'll have a lot more room to store your bike and the conductors will generally treat you a bit better. I was taking a train from Paris East to Lyon with a few people, and one couple in our group with bikes in boxes got denied boarding for second class, while others in first class had no issues.
To really see the Luberon you'll have to ride some hills, as most of the sights/towns are up in the hills (e.g., Gordes, etc.). You can also do a mostly flat-ish ride, but you'll miss many of the big sights. Last summer we stayed a week in Isle-sur-la-Sorgue and did a lot of day rides from there, most of which weren't too bad (Gordes is a pretty good hill, though).
That's another thing you could do: find a "base camp" and do day rides if you don't want to have to find lodging each night.