Its a world of possibilities as they say...
That is a pretty good point she did believe him at one point, it did affect her badly, and she will in time, be able to trust herself again through the help of others. But this is where the ending difference will lie. Now everyone makes mistakes, negative emotions can turn even the most amiable person into a malevolent jerk, but there is always time for repentance. What I am trying to say is that the girl will be fine in the end, but what about Mr. Arc? (sorry if the way of address is offensive)
Mr.Arc will not really be able to forget the incident, and is it really fair for him to suffer all his life for one mistake? Sure he deserved it, but no one should be condemned for life, just by letting their emotions go once.
What he did was unforgivable, but the punishment should not be so severe. Saying sorry will not awaken her feelings again if he explains everything in the process, e.g: why he feels it won't work out, all the times he has tried to make it work.
Coming clean will help them both in the end, because the equation looks like this to me:
Her + not saying anything = eventually happy her + miserable Mr. Arc
Her + saying the truth = Two happy persons seen after the passage of time
Not that I am saying what he did was not really something inexcusable but as an INFJ I have already been through something like this (well I hurt a friend) and I know for a fact the guilt will never go away until you say sorry. If you don't want her to feel pain again, then don't tell her the reasons but at least apologize
There may be many holes in my reasoning so feel free to show them, it helps me learn to think from different perspectives.