I wouldn't have made it a downer ending, introducing a new threat just so most of the surviving Animorphs could go off on a suicidal mission. It wouldn't hav been all parties and rainbows. It would have taken time to heal. They would have healed, though. Marco's ending would be almost the same, except he'd take proper vacations instead of morphing lobster in a pool. Cassie would become a zoologist, using morphing power to be in tune with animals. Jake would join the military. Rachel may become a cop, or get into extreme sports. Tobias would become Human, move in with his mom, and become a pilot so he can still fly.
Rachel, Tom, and the Auxilaries would live, because if you've established for 50+ books that sympathetic named characters don't die, you don't throw it out in the last book or two. Toby takes her people to her homeworld to take it back.
The war has a lasting effect on people, but they get through it over the years. One of the themes in the early books in "hope", after all. It's a war story, but it's also a kids series. You think The Land Before Time and secret of NIMH would be the classics they are if Little Foot's group got eaten and Frisby and her kids drowned in mud? I doubt it.