Battery powered sensor node power down circuit
I think you can fix it as follows: 

Put a pulldown on sysoff, maybe 100k. Just make sure it is strong enough to overpower the internal 5M pullup. Also keep sysoff connected to your IO expander. It should be configured as an output driven low. But when you want to power down, have the expander drive the output high, which will overpower the 100k pulldown, and turn the system off. 

Once the system is off, your rails will all collapse, so the IO expander will be dead, and the 100k pulldown will ensure that sysoff is now low so that startup will be possible the next time charger is attached. You will need to make sure that the IO never goes high during bootup or normal operation. For example, program it to be low before you program it to be an output.