the heater core sits in the lower box half and the ac evaporater sits in the upper case half. if you can manage to remove the lower case half in the car without having to pull the entire case, then yes, you should be able to do it without disturbing the ac lines. it's going to a difficult project though.
Aw man.....I have two Mustangs that need heater cores and both have A/C. I never cared for under-dash A/C, but I guess the '68's core would be easier to change in it had that instead of a factory unit. Luckily my system has no pressure so I could disconnect them without losing anything.
The SVO on the other hand.....half the interior has to come out.