Of course, in both cases, that is a bug of the particular reputation system, not of reputation systems in general:
1) In the Ebay case, reputation can be conditioned on the type of items and the flow of money being processed by the merchant. Someone who is highly reputable for $50 transactions, isn't necessarily so for $5,000 ones. You could also always have "anomaly detection" built into the system, which kicks off whenever the seller moves too quickly from $50 items to $5,000 and either warns users or pro-rates their reputation (if nothing else, radical behavior change could mean the seller's account got compromised...).
2) In the Bitcoin exchange case, there is currently no real reputation score for Bitcoin exchanges as far as I know. But you could have a proof of stake system that requires exchanges to hold X% of their funds available, similar to the requirements for banks. You could also operate the exchange in a reduced risk way if say, to convert $1000 USD to BTC you sequentially post 1000 $1 USD transactions and don't send them the next dollar until the corresponding BTC amount clears on the network and is safely stored in your hardware or multi-server wallet.
Not saying that there aren't fundamental issues with reputation economies, but lets give the dystopia a fair trial and assume that the non-essential problems will be solved.