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Determining the "right" fees is a separate issue; see https://gist.github.com/2961409 for my current thinking.
The raw transaction API will let you create and try to send a transaction with as much or little fees as you like, but if you try to send a 20 kilobyte transaction with zero fees you shouldn't be surprised if nobody relays or mines it.
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If you use the raw transaction API then you're responsible for saying exactly where all of the outputs go. If you create a raw transaction with a 50 BTC input and a 2 BTC output then that is a no-change, 48 BTC fee transaction. If you don't intend the 48 BTC to go to miners, then you need to specify where the change goes by adding another output.
I suppose the RPC calls could have limits to try to keep you from shooting yourself in the foot, but anybody using the raw transaction API should be doing a lot of testing with worthless testnet coins and I'd rather not start playing the "lets write lots of code to try to prevent RPC-users from being dumb" game.