Do It Again
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I wouldn't do it as you suggest. I think that active fermentation would dissipate most of the vanilla character you're hoping to capture and the beans would be mired down in the trub and yeast.
I had a very tasty version of the BVIP at NHC that i made using a tincture for the vanillla. Take two beans (per 5 gallons), split, scrape, quarter and place in 60 ml of vodka. Cover with cellophane and a rubber band and let set in a dark cupboard at room temp for a week. Rack your beer to a secondary on top of the vanilla tincture vodka, beans, gunk and all. Ferment another week or two depending on how strong you like the flavors. Good luck and enjoy, you won't regret trying this brew.
IMO, too much effort for no gain. Just put 'em in the fermenter. Primary (after fermentation) or secondary (my preference).
The will of the wisps - Ozric Tentacles