Finally did a decent effort for making a de-flickered time lapse video.
Here is the synopsis of the workflow:
1) shooting two sequences of 300 pictures with Magic Lantern's intervalmeter on my 550D (jpegs) in manual mode
2) in Lightroom, added a creative preset (color grading) and changed to 16x9 format; then exported to 2048 pixels wide jpegs
3) in VirtualDub: imported the 300 jpeg sequences and added the MSU Deflicker 1.3 plugin. Rendered to 2048 avi (huge file)
4) imported the avi into Sony Vegas; added titles and music; sped up the avi to fit the music score; rendered to 1080p mp4
For those interested, here is the older version I made, which was clearly NOT deflickered:
As you can see, VirtualDub and the free plugin do a pretty good job at deflickering!