I donīt think anyone who wants to solve things killing off the general population of the other side can be called the "good guys" no matter if they are human, mutant, kree, skrull etc.
thatīs my one pet peeve so no I donīt see Orchis as "protectors" or "good guys at all" that said as antagonist they have been quite passive but well maybe that will be addressed in the future.
but I agree so far X-writers have done a good job keeping us wondering if the X-villains will get up to something or if Orchis will reveal itīs hand so far I think they have done a good job showing reasons why some of them like Shaw, Apocalypse, Mystique, Selene, Mastermind would like to keep the status quo on krakoa but by doing so they have left behind the X-men part of the story, with the exception of Wolverine, so now that we will get a new X-men team we will get more of the main X-men povīs of things.
So far I think the writers have done a good job showing how the mere existence of Krakoa practically allows a space for redemption or at least a cease of fire between mutankind and humanity and that on itself is a good thing and still the main tension about what they will do in the future is still there but also a possibility for change.
In Magnetoīs case is interesting because this is pretty much his dream come truth so heīs 100% doing the best he can to hold it together between all mutant groups and the biggest irony would be, if the trial is a clue, if heīs the reason why it gets an schism and still I see him so convinced this is the best way to solve everything, that heīs the kind of character who would rather go down with the ship than leave it, so I am quite curious what justification will be there for him to rock the boat because it must be pretty stron and I believe it involves the well being of mutants on Krakoa.