I don't use MobileMe anymore, so I may be wrong, but I have done a lot with WebDAV and CalDAV and MobileMe in the past...
My understanding is that OmniFocus uses WebDAV to sync both its own data and the iOS calendar. It does not use Sync Services on iOS.
MobileMe is used purely for WebDAV. When you tell your iOS device to subscribe to a calendar, it's subscribing to the calendar via HTTP, pointed at the WebDAV server. MobileMe doesn't really know or care that it's a calendar. It's just a file.
Your "official MobileMe" calendars are synced independently of OmniFocus.
The only feature of OmniFocus that could possibly be broken by a MobileMe change would the desktop iCal sync, configured under the iCal tab in OmniFocus Preferences.