At the simplest level, as I read it, it was a matter of split-second timing. Haman had been standing near Esther, begging, and half a second before Achasheveirosh walked back in, he tripped and fell on Esther. Esther, having seen the whole situation, likely realized that he had tripped. Achashverosh walks in and just sees Haman on top of Esther (or at least on her couch) and reaches another conclusion, and immediately starts shouting.
At that moment Esther most likely doesn't think it's wise for her to speak up and say actually your majesty, this horrible scoundrel is horrible for all sorts of other reasons and I want him gone, but he wasn't also trying to rape me. (Esther is generally smarter than to try correcting a king with a very fragile ego and short temper.)
There's the medrish that an angel kept making Haman trip to ensure Achashverosh would see exactly what he needed to see ... but what happens in the split second that Achashverosh walks in is still the same.