2002 Honda CRV Air Conditioning Problems

I have a 2002 CRV and the air conditioner went out a year and half ago. We decided not to get it fixed due to the cost of over $1,200.00.
A loud noise just developed in the water pump area of the motor so our garage changed the water pump. The noise went away for about 15 minutes as we were driving home from the shop. However, now the shop is saying they have to replace the air conditioner (still over $1,200.00), that we shouldn’t drive it until we do and that they won’t warranty the repair due to problems with Honda CRV’s.
Can we do anything so we don’t have to do the repair and if we don’t will any other part of the car be affected such as engine cooling or windshield defrosting?
Thanks,

Let’s start with your question first. No the AC has nothing to do with the water pump or that repair. Yes your defogger will be effected but that’s about all. I’m not sure what the mechanic is getting at by saying he won’t warranty his work.

As for the AC repair price, it seems very high to me. I just replaced the compressor on my 2004 crv and the price of parts/freon/o-rings was less then $400 ($300 was the compressor and dryer ). I did the work myself, but still most shops charge 7-800 for this job. So your still about 500 high. Time for a second opinion.