[Lizard]

OmniFocus has to be able to handle getting interrupted mid-sync, because this happens a lot on the iPhone. Your data has already been saved locally, so it won't get lost. You'll just need to sync it when you launch OmniFocus the next time.

However, it would be a better experience if we let you cancel the sync.

Meanwhile, syncs should be getting a lot faster with the latest builds. If you're having sync times over a minute for really minor changes on a standard DSL or cable internet connection, there is definitely something going wrong with your file.

Sync all your desktop computers, then run the attached applescript on whichever one has the most up-to-date info.
(You can run an applescript by opening the "Script Editor" application, opening the script file, and pressing the "Run" button.)
Next, open up your iDisk (or whatever location you're storing your sync database in) and rename its copy of the OmniFocus database to "OmniFocus-Old".
Do a sync from the machine that you ran the applescript on.
Launch OmniFocus on your phone and start a sync; when asked whether to use the 'local' or 'server' copy, choose 'server'.

Your syncs should now take a reasonable amount of time again.