You can generate a 1MB block with only free transactions in it and it will get accepted (maximum block size is 1MB, although the standard bitcoin client will never generate blocks larger than 500K).
The problem isn't the pool payout-- the problem is that people participating in the pool end up with wallets full of tiny (e.g. penny-size) transactions. When they go to spend those tiny transactions, they're bundled up together to make a transaction that is small in value but large in size.
Pools can mitigate the problem by requiring larger minimum payouts (e.g. 1 BTC instead of 0.01 BTC).