Yes I believe the CoinShuffle protocol (with some slight changes) would be compatible with the mini-blockchain scheme. The only issue I see with CoinShuffle is that it requires the generation of fresh output addresses, which will bloat the account tree. CoinShuffle kind of just spits out your mixed coins into a fresh address, and if I'm not mistaken the level of anonymity achieved really depends on how many people participate in the mixing process. I don't think it's a perfect match for the mini-blockchain scheme but it may prove to be the best possible solution because I'm not sure something better exists.