Spoilers for Good Omens 2 below.
Yes. It sucked to see our favorite pair Aziraphale and Crowley being pulled apart at the end of Good Omens 2 - but, for the sake of the longer term releationship, it is a necessary development.
'Why?' you might ask. Why must our hearts be torn apart like that? Well, because things are changing for Crowley and Aziraphale. It took them some millennia, but they've grown as beings, and, as we've seen with Crowley's confession, they are finally moving slowly (oh so slowly) towards each other.
And because they are moving towards each other, we need to see them apart for a bit. The reasons behind that argument are two pronged. First of all, now that we've learned, over two seasons of television and clips from their thousands of years old relationship, who they are together and to each other, we need to see who they are apart. They've influenced each other immeasurably, and now that they're split up, we'll hopefully see those changes even more starkly as Aziraphale finds himself in a new position of power in Heaven and Crowley finds himself alone on Earth.
The second prong of this argument is that all big change comes with challenges. The show is clearly leading to a romantic conclusion for these two characters, there will of course be some resistance involved in getting them to change what has been working for them for literally thousands of years. In season 1, we've seen Crowley and Aziraphale unite against Heaven and Hell, and in season 2, we see them united and then divided by the same. In season 3, we need them to struggle against and then overcome their own selves to finally be together. We know that it can be done, seeing Beezelbub and Gabriel's happy ending, we just need to see Crowley and Aziraphale allow themselves to realize that too.
Sure, it's tough to see our faves struggling, but it's clear that they're not quite ready for it yet (though one seems much more ready than the other). While we may be waiting for a long bit until Good Omens 3 gets a renewal (and even longer before it airs), it's good to know that the show is poised to give these characters an arc, not only together, but also on their own.