First, I am so sorry for your loss, I can't imagine how hard this is for all of you.
I am shocked at how many people would tell they kids the whole truth. No way. They are 6 and 9- way too young to bear this burden. If nothing else, they are not developmentally ready to process that information. Not to get all psychology nerd here, but they think in an operationally concrete way. This means that they can't quite get the nuance of the situation and think in an abstract way. They can't ultimately accept that the dog ate the dough, they didn't feed it to him. And that it was an accident, etc. They just can't handle this information at this age.
I think you did an amazing job with your kids. You didn't just lie, you did tell them that the dough was not good for him. But you framed it in a way that leaves an additional step that was not their fault- his age. I would have done the same thing. You did not miss a teachable moment. The dog has passed away, I think they get it. Good for you for softening the blow for them.
There are lots of good kids books on the loss of a pet that you could get from the library and read together a few times. This will also help them process things and heal.
Another idea is to have them draw pictures of the dog, ask them to draw the dog and include what they loved most about him. Or you could have them draw pictures for the dog and send them to heaven. When our cat died my daughter was 8. We all wrote notes or drew pictures to send to her in heaven. We tied them to balloons and let them go (though we found out you might need two balloons- the paper weighed one down!!). It was very healing for all of us, and helped my daughter express what she was feeling through drawing. Just a thought- something ceremonial like that can help. Or plant a tree or something?
I hope you all heal and are able to remember how much your dog was loved and the sweet memories, not the sad end. And again, I think you did just the right thing. Good job, mama.