It's not a perfect system - no system based on all human beings telling the truth at all times ever CAN be. And with no EVIDENCE (there's no physical evidence, questionable circumstantial evidence, and any testimonial evidence extracted from the child is going to already be tainted), other than the remote possibility of any salvagable expert witness testimony which MIGHT only be able to SUGGEST that "something" took place, there's not much to build a case on. None of which is intended to discredit the child, or even question whether something occurred or not, only to point out that criminal charges and criminal cases are based on what can be presented to judges and juries - and there's little or nothing here to work with - and certianly nothing that is going to take a criminal case to the level of "beyond a reasonable doubt".
The best you're likley to get out of this, IF you can get a forensic interview done, is that, depending on the results you MIGHT convince a court to order that visitation be ONLY with the mother, such as in a supervised setting (meaning, either mom gets a place of her own where she can visit the child without the suspect around, or, mom gets to travel to where the child is if she wants to visit, to ensure the child isn't exposed to the suspect).

