You're right that Circle can blacklist USDC, even when it's used as collateral in protocols like MakerDAO.
That's one of the trade offs with DAI today, since a portion is backed by USDC. However, not all DAI is backed by USDC, there's also ETH, WBTC, and other decentralized assets.
The risk is real, but it's more distributed compared to holding USDC directly.