Yeah. 1 GH/s is way too much for some of these coins.
Part of my calculations include looking at past results of profits. So if there is a coin with some problem, that will be accounted for. I don't think pre-mining like you say would be good, because you'd lose out on that 2 minutes of profit. And past results are probably a good enough indicator.
I really want to split up the hashrate like you say. It's going to be hard to figure out how to make the payouts fair though. Do I randomly choose the people who get to mine on the smaller pool, or is it who has the lowest reject rate? And do their extra profits get distributed into the main pool?
It's a pool, so all of the profits would be distributed into the pool regardless of the coin that particular miner is mining.
2 hour period:
Miner A is mining FTC
Miner B is mining CAP
Miner C is mining DCG
Miner D is mining CRAP
Miners E-Z are mining LTC
For that 2 hour period they all get shares that are distributed amongst all of the coins being mined. I am sure there are flaws in that idea since I have never operated a pool.