Probably not...
There is a distinct possibility that the flip flop will be reverse powered through the pull up resistor even if you remove Vcc2.
A whole lot depends on the logic family of the flip flop, and what else is powered on Vcc2.
Its all a very bad idea.
Your best bet might be to place a low power mosfet between the flip flop and microcontroller.
When you kill Vcc2 the gate will have nothing to power it, and mosfet will remain off.
When the gate is high, it will pull the input to the microcontroller low.