well... it's fine to use a 5 gal fermenter and not fill it all the way, I do this and don't secondary so my ales are in primary for 3 or 4 weeks (no autolysis issues yet and if you move 'em someplace chilly after the active part is over they come out really clear). BUT the reason I am safe is there is there is a CO2 layer over my beer from the big ferment activity. If you are racking to secondary you would not have that.
I'd say in the future, get two yeast packets (dry is cheap) and pitch into two separate primaries, wait until active is over, and then chuck your beans into one of the two and leave it a few weeks.
I don't know what would happen if you just went for it and split your current batch up, I've never tasted secondary-osidized beer and I don't know the danger level. If you wanted to be anal about it you could find a co2 source and purge the headspace in your secondary before closing. An easier idea might be to just do it all in one secondary, then at bottling time, prime and then bottle/keg half, then add some vanilla extract before bottling the second half. Only issue is does the vanilla extract have fermentables in it... might want to know that to avoid grenades.