Wow, that's a tough one without using a hardware based or dedicated plug-in. Is the shot needing to be fixed very long?
How are your photoshop skills? If the shot wasn't long, you might want to try exporting a frame movie or a folder of tiff or targa still image sequence files, opening them in photoshop and creating a custom batch action to level out the flicker. Batch actions in PS are a tedious but powerful tool when you can't fix something any other way, but they are labor-intensive even with extensive automation. I don't know what else could be done, I assume you already played with field order to make sure that's not an issue.
If you find a fix please post a follow-up message here for the next guy that encounters this problem. Best of luck.
Thanks for the comment. It echoes what others say, too and I'll definitely keep it in mind.
For now, I'm going with an old low-fi chestnut that I've worked with before : place a copy of the clip above itself in the timeline, offset by one or two frames at half-opacity.
I'm not sure how well this would work with a lot of action in the frame, but the clip in question is a video-portrait. It does a pretty good job. I'd recommend anyone with the same problem give it a crack, too..