To separate the power nets, you could consider stupid (low drop) diodes. One diode from normal V+ to Vcc pin of the controller, another one from temporary power to Vcc of the controller. You must consider carefully if the drop across the diode under normal operational conditions is acceptable. Shottkys have about 0.1 to 0.2V drop. Using diodes, you will not have to use physical breaks in the nets, you will not have to worry about desoldering solder bridges or opening switches. Also, there would be no risk of anything blowing up if you by accident applied both supplies at the same time.
Separating the serial interface could be done with a simple resistor, provided that it is low enough value to make it possible for the normal Rx interface circuitry to pull down the Rx pin of the processor down hard enough to have a solid '0'. The ISP circuitry applying the alternate data to the Rx pin directly should be low impedance enough (for instance a direct push-pull output) so that the resistor becomes a reletively high impedance barrier. The resistor value must be high enough so that current through the resistor during ISP stays low. Again, this could provide you with a 'separation' without any real breaks, and no risk of short circuits because you forgot to open a solder bridge.