This issue affects all versions of Exchange that have EAS (2003, 2007, 2010). The symptoms are random, but typically occur on mailboxes with high item counts (inbox/calendar are the usual culprits) and/or are already comprimised perf wise. In other words: if your server is already near the tipping point, this will bring it over the edge. Just because you don't see any perf issues because of the firmware update doesn't mean your user base's iPhone population shouldn't apply the config file. Apply to all your iPhone users with the iOS 4 update.
Exchange Server 2010 gives you the ability to quarantine devices based on the user agent until the owner contacts the admin and confirms they've applied the update. Yes it's time consuming, but it's a lot better than having your server down. :)