As you've probably figure out, in order to get the heater box out you have to disconnect the lines going to the evaporator.
I'm assuming you're using the right disconnect tools? The connections are probably rusted pretty good, but with some PB Blaster and a fair amount of working the fittings to turn them back and forth as much as you can, it is possible to eventually break them free. You can also use a pick to yank out the garter springs with eliminates the need for the tools and you can get replacement springs at a good parts store.
Of course presuming you've already safely evacuated the A/C system, if the A/C system was bad already you could just cut the lines with a sawzall or tubing cutter. I've done that more than once and just put in a new evap core, and replaced the lines when it was time to get the A/C working again.