This is a common problem with device obsolescence. If you really do want to continue using that exact part then you are restricted to using the last version of the tools that supports it.
The EPM7128AETC100 is pin-for-pin and timing compatible with your device and is supported by (relatively) up to date tools. I recommend you consider reworking your board with one of these and using Quartus 13.0, which supports it.
Editing a binary is a non-starter as Altera have never published the structure of these files. Don't waste your time.
Cheers,
Alex