i think you will be ok leaving the heater matrix as is.. You probably know from looking at it that the alternator and where its mounted iis different. So you need an alternator off an non-ac model and its brackets. I'm pretty sure you should just be able to disconnect is all and stick the new alternator on and you'll be fine. After the heaters etc work without the AC on. But you may want to consider taking the whole lot off so you have a complete AC setup you could sell on, probably for a fairly good return.
I think you will struggle to find exact answers here as my seicento is the only one i have seen in the UK with Aircon and the forum is mainly UK members (but not all!)
But to get it off is pretty simple if you get under the car and look at it. Download the Seicento Technical Manual fromt he download section on here, its pretty well covered how to remove it - Just remember that you should be getting the system properly emptied and not just open it atmosphere, thats really really bad for environment!!!