I'm tempted to believe the same thing. But then he wrote a lot of the opposite from Air to Little Busters! so I don't know what his belief is. I don't know if he's pushing his belief into the story, or pushing it aside just so he can write a tragedy. And yeah if I was confronted with the same situation, I would probably have adopted Tomo.
Keep in mind that I believe the tragedy story and end itself is very well written. Accepting and moving on is a big theme in Tomoyo After (and Clannad), and I echo Ishiki Hikaru (Tomoyo's CV) that the story will seem deeper and more understandable the older you are after you've already lost something.
My objection is that he wrote a separate route (and given the setup, the one most likely to be picked on first playthrough) with them backing off and adopting Tomo. And he wrote it like a bad end. It shouldn't be. Accepting that blood family didn't work out and moving on with an adopted family is still accepting and moving on. He wouldn't be breaking his theme. In fact it would've made a good story as another type of struggling and successfully moving on with help from a family, his theme after all.
He could've wrote two, equally valid routes.
Or if he really wanted to write a tragedy, then he should've made it so that there's no choice option.
Either way this would have made Tomoyo After solidly in my top. But he didn't. He just had to write a supposedly-bad end that went against everything he wrote up to the point.