Well, you can't really prevent them. But what you must do is detect them and not rely on any transactions if you are on the minority side of a split. You detect netsplits by waiting for validations before you rely on the contents of a newly-generated ledger. So if there's a net split and you are in the minority, you won't get validations from a significant fraction of your validators and thus won't consider any new ledgers fully validated.

Significant netsplits should be pretty rare because all it takes is one server that can connect to each side of the split and the split is healed. I suppose a natural disaster could cut off a country leaving only the clients and servers in that country talking to each other.

Now that I think about it, something like this could be easily added to Bitcoin. If the network hash rate seems to have drastically decreased, you should stop trusting transactions no matter how many confirmations they have. Does Bitcoin do anything about this? Does anyone think it's needed? (It's less of an issue with Bitcoin though. It would take a two-plus hour netsplit to fool you into thinking you have six confirmations if you're in the minority. Ripple aims for faster fully-confirmed transactions so has to detect even transient splits.)