I'm not sure Paul, Madara mentions the even Hashirama's enormous chakra belonged to the Shinju and not that part of Shinju's chakra is in Hashirama. He mentions that "all the chakra here..." all, not portions, literally all.
The moon might be the key, since the GM/Jyubi/Shinju was imprisoned in that stone and when the light shone on the stone, the stone reflected this light, accompanied with Shinju's chakra (the Jyubi was able to gather more power on it's own, so it's possible that it was regenerating slowly some of it's power anyway), the moonlight shone on humans and other creatures, which in turn gained chakra from it... well in many myths the Moon is the source of many supernatural powers, so this might be another explanation, at least it would explain how Ninja Animals were born, since they couldn't have been descended from So6p like Human Ninjas, right ?
How big the chakra amount had to be in that fruit, for Jyubi to went on a rampage in order to retrieve it ? But the problem is that while Shinju might have been using chakra (or perhaps rather Senjutsu Chakra), the Jyubi itself was using only NE as Naruto mentioned.
So it should be like this:
Shinju---(deprived of chakra)--->Jyubi---(deprived of NE)--->GM ? Damn this Mezoevolution .
As to why people die when Chakra is sucked out of them ? Well, because it became essential for them to live. From the looks of it, Ninja are not Humans, since anatomically they are born with chakra channels, points and the like that normal people aren't, their bodies exist, work and live based on chakra circulating through out them. Basically, the organism relies on chakra, it adapted to it at such a level that it can no longer live without it.
BTW, the amount of jokes about the Uchiha Tablet on the net is enormous, lol . One of them compares it to Matrix, you know how like at first you only sees letters on the monitor, but with a good "eye" one can see the world inside and what's happening in it . I sure would like to see it animated . Most of them compare the Tablet, with a Tablet , or flash drives and the like .
Now that I think about it, the Tablet is supposed to be really old, so how come Madara, Sasuke and others understand the language it was written in ? Shouldn't the language transform a bit, or even die out in time ? Or is it that when a Sharingan looks on it, it really shows pictures instead of letters (well this would explain all the pictures that are shown when Madara tells those stories ) ?