From what I understand you would like to control GPIO1_9 with core 0 and GPIO1_10 with core 1. You are able to access different pins from different cores individually. However be careful no to attempt to use the same pin at the same time this may cause some issues in your application.
In addition, reading the GPIO1_9 should not affect the pin next to it, so it should not be a problem of changing the value on accident.
The grouped GPIO pins have a specific purpose to work as an interruption.
If you need examples of how to initialize pins on different cores let me know.