Do you plan on
ever using the air conditioning again?
If so, I would close the valves on the manifold (the part that bolts to the compressor; 2 bolts hold each manifold on) and then disconnect and secure the lines elsewhere.
But, if you intend on permanently ditching the A/C (not what I would do from a comfort and a resale perspective, but to each his own), you can remove the lines altogether. This'll get them out of the way for any other engine work you need to do. Prior to pulling the heads and whatnot on my truck, I removed every component of my a/c system in order to get it all out of the way (also to flush out each individual component prior to getting the system operational again)...it actually wasn't that big of a task.
If you pull the lines and just leave them hanging, the a/c system WILL die (seals hardening up, water entering the system and rusting things up, etc)...so, I would either leave the valves shut and keep the charge, or ditch it entirely.
Whichever way you go, make sure you have the a/c system (or just the compressor if you decide to leave the lines on) evacuated by a shop before you go any further. This is for legal reasons. Or, if you still have an R-12 system and there's someone nearby with a vacuum pump and a need for a recharge, maybe you could transfer the freon to someone elses' truck? R-12 is getting pricy these days...
Just some thoughts...good luck!
Regarding the heater, you can pull the a/c evaporator (where the two a/c lines attach in the heater box) and still have a properly functioning heater. However, you'll want to seal up the holes where the a/c lines went in...
BTW, Mel, if you can't get his core, I still have the old compressor out of my truck sitting around doing nothing...the clutch is bad, but it was otherwise in decent shape when I pulled it. In retrospect, I should have just pulled the clutch off the compressor from Cops' truck and installed it on my compressor, but I didn't have the tools...such is life, eh?