Hello there, the author chiming in here. Thanks for giving the story a read.
(Spoilers to follow for those who have not read it yet.)
The disc is the conduit by which the entity is able to interact with our world. It established a connection to Bonnie's soul through the disc, so when she shattered it, she was able to sever that connection and save herself, but the entity is still safe in Sonic's world, and will eventually cause another copy of the disc to manifest somewhere else in our world.
As far as the defeat of the monster goes, I went for a "toss a light into the future" approach. It wasn't seriously hurt, but events have transpired, information has been gained by Sonic, and the hope is that what has happened here has caused some gears to start spinning, and events may have been put into motion that might eventually lead to the final defeat of the monster.