You can't ruin someone's life on the basis of "balance" of probability. A rape conviction will almost certainly mean prison time, serious problems getting a job in the future, etc. You can't inflict that on a "he said, she said" balance of probability.
I think the main problem is that we don't have different classifications of rape.
For cases like this, where there was no violence involved (from what we can read), maybe we need a new offence of something like "non consentual sex" with a lower punishment level, that a jury may be more inclined to convict on?
Or perhaps, given the obvious problems with consent, especially on young girls, we should make ALL sex with a minor illegal, and convict everyone where there is evidence that sex happened, regardless of consent, but again, not for "rape", but a new offence of under-age sex. Obviously that has the potential to catch people who ARE consenting, but after all, under age sex IS illegal.
It's the fact that "some" cases of sex maybe illegal are tolerated/accepted despite being underage because there is clear consent that poses the problem as under-age sex has become accepted and normalised, so the line where it becomes non consentual/rape has very muddied waters these days, especially when we factor in the imbalance of power when one party is older than the other, or where drugs or alcohol is involved, etc.
If we made under age sex illegal always, regardless of consent, and prosecuted for it, whether or not there was consent, the "consent" issue becomes irrelevant. The boy IS committing an offence, whether or not it's consentual, so if the girl makes a complaint, and the fact that they had sex becomes factual (from forensic evidence), then there is no doubt the offence of "underage sex" has been committed and the boy can more easily be found guilty, but for a lesser punishment that won't ruin his life in the same way that a rape conviction would.
Not saying it's right, but it's one possible option to deal with this kind of issue which seems to becoming a bigger problem as more and more under-age sex seems to be happening and the issue of consent has been an issue in all rape cases for decades. This may be one way of dealing with a particular problem.