In practice it doesn't seem to matter. For example btc-e.com who accepts both bitcoin and litecoin for trading makes you wait 3 confirmations for bitcoin and 6 confirmations for litecoin. So you are correct that 1 litecoin transaction is not as reliable as 1 bitcoin transaction but they are not making you wait 12 litecoin transactions.
Given that btc-e has a lot to lose on double spend attacks I think it's a good measure of how these two currencies are playing out in the market.
Comments
In practice it doesn't seem to matter. For example btc-e.com who accepts both bitcoin and litecoin for trading makes you wait 3 confirmations for bitcoin and 6 confirmations for litecoin. So you are correct that 1 litecoin transaction is not as reliable as 1 bitcoin transaction but they are not making you wait 12 litecoin transactions.
Given that btc-e has a lot to lose on double spend attacks I think it's a good measure of how these two currencies are playing out in the market.
The propagation times are very important here. You can get away with faster if and only if the network communications latency is low enough.
If blocks are too fast you start getting very large reorganizations.
Today litecoin has almost no transactions, so its lower interblock time is not a problem... Yet.