The flower planting doesn't preclude them from later depicting her as not on board with Krakoa, but with all the setup Hickman did for Marauders elsewhere in HOXPOX, it's hard to imagine why he would have written Kitty into that sequence in the first place if Kitty's role was going to be as a Krakoa skeptic. (It's not like Marauders took shape in between writing HOX #1 and POX #5; I think Duggan and White have said Marauders has been in development for a year.)
Also we've seen on the Krakoa map that Hellfire Bay has a "Red Keep", so if Kitty isn't living on Krakoa at the start of Marauders, I bet it doesn't take her long to relocate.