I'm not sure if it is organic or not. I do remember that the Metal Gear Rays in MGS2 "bled" as well, and there was no mention of them containing any organic material. Personally, I think it's just artistic license, meant to make the Metal Gears seem more like monsters (this, by the way, is consistent with Metal Gear Rex, Ray, and the Shagohad "roaring").
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it's hydraulic fluid... mechanics have it colored red so that they can see it when it's broken.