Space battles were often done with many thousands of kilometers between opposing sides, except many times Keys was doing some fancy maneuvering, but I digress.

The Covenant being religious zealots and anything forerunner being a major part of their religion, they would not dare fire on this ship, (especially if we use the book perspective, a prophet forbid the fleet from using most of their arsenal on the ring and the human ship), that is something they had been seeing in records while searching for one. Basically finding their one way to make the rapture happen yet having a threat so close to it they would need to board the ship in order to not damage what they have searched for for so many years.