You have no reason to attempt to justify your actions. There is a difference between what the "law" allows and what people think is "safe". In this case, many states permit humans to ride in 5er and TT (some states don't). But I'm pretty sure that every states considers a dog "property". And "property" can be transported in a trailer or a 5er.
Legally, you are well within you rights to transport the dog any way you want. There is nothing cruel or unusual transporting (your property) in a trailer especially when you've taken all the precautions you have.
People do get emotionally attached to their "property" (I know, I'm one of them). So to justify your actions is not needed. Do what you feel is best for your situation. 
My neighbor has a Mastiff and that is one BIG dog! He's like a gigantic galloping horse!  He's about as lovable as anyone can imagine, but STRONG and .... well ... has a tendency to slobber over everything when he gets excited.
My little Dachshund chases him around the yards and through the fields behind our houses. That short legged little thing's legs are just spinning like tires on wet gravel!  And that big old critter just gallops like a Thoroughbred Triple Crown race horse, so graceful!  One would not think the little guy would chase the bigger guy, but this is how they play.  Yup, that's one big dog.
So, with a baby coming along, you're priorities do have to be in the right place. The dog has no choice but to ride in the trailer. And you're OK to do that. Don't let the "nay sayers" guilt you. Until they've walked in your shoes, I wouldn't give them a moment of my time.