But you still need to know when the coins arrive right?

I'm not sure how it's possible to run an online shop that accepts BitCoins without having a node or using something like MyBitcoin. Unless the merchant does it all manually.

Perhaps the real solution is to try and organize people to integrate BitCoin with popular shopping cart software. I know some of it was already done but did the changes make it upstream?

As to keeping the node secure and up to date, hopefully it's secure out of the box and making it auto-update (even on Linux) is probably easier than many alternatives. First step would be to have it provided via an apt repository hosted on bitcoin.org (the official distributions are way too slow).