NO, that is absolutely a lie. For one thing, your DH's commanding officer has no business knowing about the medical decisions you make for your child. You should really, really complain to someone in charge at the hospital. Not only did they lie to you, but they were threatening you. You didn't "slip through the cracks", they had to let you go because they were telling a lie. They just pretended they forgot about it.
Tricare could never have any kind of agreement with a hospital about what medical procedures will be performed on YOUR child. That's such a load of crap I can't even believe they told you that. YOU make medical decisions for your child, not Tricare.
We are a military family. Lots of military families have been bullied by base pediatricians. We haven't had much of a problem, but you should be prepared for the two month check up. It probably won't be an issue, but if it is, YOU ARE THE PARENT! Do not let them bully you, threaten you, or anything else. And if they do, report them to the clinic CO. I am not joking about that. If you take her in for your DD's two month, and they threaten you with CPS, say you need a letter from your CO, say Tricare won't provide coverage, or ANYTHING even remotely out of line, tell them, "We are going to complain to your CO because you are harrassing us." That will shut them up really fast. Their CO will be on your side, because the doctor will be wrong. TRUST ME on that. Don't take sh*t from any base doctor. If one harrasses you, and you don't complain, you will be complicit. You will be allowing them to continue harrassing yourself and other parents. Don't be afraid of them and don't put up with it.
I doubt you'll have a problem, but I really like to scream that from the top of my lungs, because so many military families live in fear that base doctors are going to report them for neglect or something stupid like that. And the thing is, if they're threatening you, and you allow it to continue, they might really do it. But if you follow up with the CO immediately after they pull some stupid BS like that, they won't be able to do it. For one thing, the CO will be all over them about being idiots. And for another thing, it will be on record that they harrassed you and tried to intimidate you, so it will be obvious they're only trying to exact revenge if they try to have you investigated.