@Meanlucario
Chakra also had a long history in-universe of being a shameless liar and con-man who’ll say anything to manipulate people into doing what he wants. His main claim to fame in the stories so far is manipulating another character into an emotionally abusive relationship and deliberately damaging his friendships with others to keep him from people who could realize he was being used. He spent most of life as a professional parasite who found gullible or vulnerable ponies, attached himself to them and promised them everything they wanted to hear while leeching everything he needed.
He’s stopped doing that by that point, sure, but Starlight and Sunset have no particular way to know that. From their point of view, it’s the word of an old family friend – whom they have known since before he could speak – and the child of one of their closest friends versus that of one of the most manipulative and untrustworthy ponies in town. They have no particular reason not to trust Moondancer, unless that are for some reason judging him using the character of a biological father he has interacted with once in his life.
Further, it’s worth keeping in mind that their daughter just died. Neither is going to be in a rational frame of mind for quite a while.
The only thing against Moondancer that they have any way of knowing is his terrible relationship with Trixie, which is still mitigated by the fact that a) this does little to impact the current situation, and b) he has a much better relationship with Maud – there aren’t, at least, any depictions so far of him having anything short of a perfectly cordial relationship with her.
Lop’s universe certainly has its issues, but this is something of a reach.