I just ran into the same problem while working on the Moneychanger project for open-transactions.

A solution is to use getrawtransaction to check if requested money was sent to the p2sh address in the first place,
then getrawmempool to see if it has any confirmations yet,
then getblockcount --> getblockhash(count) --> getblock(hash) --> getblock(block->previous) -->... to iterate through the blockchain to figure out how many confirmations it has.

If you don't know the txid you could scan the blockchain for new txIDs and use getrawtransaction on each of them to figure out if any outputs were sent to the multi-sig address.

Haven't implemented it yet so I'm not sure if it will work like this but so far it looks like it could imho.

This all seems very hackish and error-prone to me so I hope we'll soon get proper bitcoin API support for that kind of transactions.