This isn't a hard problem to solve at a technical level. Have the nodes keep track of the version numbers they see on the network. When X% of the network has upgraded to a version which supports the new rules, and when Y% of the miners indicate their support via coinbase flags switch to the new rules. Until then use the old rules. Let the users decide when and if to switch.
So if my client only ever connects to a subset of clients that have chosen not to upgrade, then my client won't know to make the switch when the rest of the networks switches?