Using bitcoins JSON RPC, how can I confirm a transaction I published? I have created, signed and sent a raw transaction via bitcoind RPC. Now I want to wait for it to have n confirmations.

Considering transaction malleability, I can't just check the "confirmations" field returned by gettransaction, because the transaction with that particular txid may never be accepted, in case an equivalent transaction with some other txid was accepted instead.

So, what is the canonical way, using bitcoind JSON-RPC, to check if an equivalent transaction was accepted in place of mine? What calls are better suited for the task?
You can use the listtransactions JSON-RPC call to get the complete list of transactions that have to do with your addresses. This includes both sends and receives. You can filter for the transaction you're looking for by the category (should be "send"), address, amount and time. The txid and confirmations in this RPC call should be what's actually included in the blockchain and can be relied upon.

For reference, here's what the RPC call looks like:

[
{   
    "account" : "",
    "address" : "1ENnzep2ivWYqXjAodTueiZscT6kunAyYs",
    "category" : "send",
    "amount" : -0.00040000,
    "fee" : -0.00010000,
    "confirmations" : 34055,
    "blockhash" : "000000000000000019313300fa20943b3974a97c1da2de6de13ea1281f77097f",
    "blockindex" : 414,
    "blocktime" : 1404861981,
    "txid" : "8a1f0f07fb397b2aa0e77995723f2dac9aee7df63a6f05a7db7d168d62a60f94",
    "walletconflicts" : [
    ],
    "time" : 1404861981,
    "timereceived" : 1412296394
}
]