The MuPDF part is separated from the rest of the code as a completely separate file communicated to over web workers, so the separation means the rest of the code does not need to be open source.
So that is not correct workaround at all for AGPL licenses. By moving the MuPDF logic into a Web Worker, you are still providing a "modified version" of the program to the user to interact with. The "separation" via a Web Worker does not change the fact that the user is interacting with a system that includes AGPL-licensed code.