Even using bitcoins for legal things leaves you little recourse - this is the whole point of bitcoin. When you avoid government regulation and oversight you also avoid the protections it gives - this should hopefully be obvious to anyone.
If you have a legal entity behind something, like say, bitpay or coinbase, you can take legal steps if they screw you over. You can take them to small-claims etc.
And if you don't trust some entity, you can use escrow with bitcoins, it's possible to setup a transaction where the escrow provider has no way to get at the funds, but can just release to either of two addresses (back to you or forward to the merchant). But of course, the escrow provider would also be a legal entity, otherwise you'd have no recourse against them if you feel they unfairly resolved a dispute against you.
Bottom line is, if you engage in legal business, with legal entities, and take appropriate precautions, you are no less protected than using national currency and chargebacks. If you don't, well, you've got nobody else to blame but yourself.
Feel free to talk to any fraud investigator and ask them just how common this kind of thing is. They spend their whole work day tracking these down, after all.
Please look into what escrow means. Of course you can do business with an entity you're not sure is legit. The assumption is that you trust the escrow provider, and the Escrow provider is trusted by the merchant. So, the critera of trust for the escrow provider, is quite a bit higher than a random online store.
If carefully select the escrow provider, check their business registration, make sure there's a legitimate entity behind them, this makes dealing with possibly fraudulent entities as safe as with fiat.
1) You could ignore all technicalities and simply send the coins to a third party which releases it back to you or forward to the merchant. That's probably the least recommendable way, but is the easiest to explain.
2) A smarter way to do it is to use bitcoins transaction script that can process multi signature transactions, which can work in a way that if A wants to send B money, he can setup an address that can only withdraw coins from if C also signs the transaction. This method is supported by Electrum and by the Blockchain.info wallet.
You don't really get a choice, and you carry the mandatory cost because merchants roll the cost of chargeback fraud, CC fees and banking fees over into your purchase price, no matter if you think you'll need the added service or not.