When I made my video. I used LR Timelapse (back when it was free) to deflicker the RAW's and export to JPEG. I then used Quicktime Pro to generate full size (16 mpix) ProRes video files which I put in Final Cut Pro 7 and then graded with Magic Bullet.

If I was going to do it again, I'd definitely look at Sequence by Frosthaus to do the deflickering and video sequence generation.

http://frosthaus.com/sequence/