I'd think - someone correct this if it's wrong - that you'd have to make sure that the L and R impulses are used on seperate tracks (or panned seperately on a stereo track, if your editor will do that) to basically provide a stereo reverb result.
Again, I'm no expert at this topic, that's only an edumakated guess on my part. There's got to be someone else here who has more experience with making IRs that could speak more authoratively on that.
Not speaking from an incredibly experienced standpoint on binaural technology, but having worked sporatically with binuaral heads partly thanks to my time at Full Sail and a couple of others outside of that...
I'm pretty sure most binuaral assemblies like this should be split already with two outputs for both mics respectively.
From what I remember, the binuaral heads I had worked with where essentially two mics inside a fancy molded foam designed to mimic the human head. At the bottom, you had whatever adjustment controls you needed and two XLR outputs.
My only thought about capturing impluses with binuaral setups is to expect it to sound somewhat different than your standard stereo micing technique.
I would expect alot more seperation between your left and right channels with a bigger hole down the center of that stereo image. That could be good for the mix, and it may not. It may give the illusion of having a wider stereo field since your imitating the way the human ear picks up sound.
Again, that just depends on how you go about micing. I would expect it to sound loosely similar to spread pair micing with a sound treated divider between the both mics. It's just different phasing, imaging, seperation, etc.
I've never sampled impluses, but I would expect the EQ response of those mics to affect the quality of your impulses. So if I had the means to capture a room exactly how it is, then I would make the effort to rent reference grade mics.
I still say it's worth a shot. A little more experimentation dosn't cost you anything.