I was diagnosed with Osteolysis of the AC Joint back in 1999, along with a Labral Tear. I opted to have the surgery. The Orthopedic Surgeon cut off a small piece of the distal clavicle (clavicle resection). If he told you he had to remove the entire joint completely, that probably scared the s*%t out of you. Talk to him again and make sure you know and understand the procedure completely, and that will ultimately help you make the right decision for you. I had a well respected orthopedic shoulder specialist perform my surgery, in fact, he had operated on many pro athletes for the same, and other injuries, so my level of confidence in him was high. In most cases, when it occurs in one shoulder, it will eventually occur in the other. I had to have an incision about an inch and a half long due to a prior separation of the same shoulder years earlier, otherise the incision could have been much smaller. Recovery time was relatively quick, in fact I really didn't notice pain, only numbness and swelling for a while. Keep in mind though that the Labral Tear repair which was performed arthroscopically (and at the same time) required the longest recovery, and more pain. This may have drawn attention away from the clavicle resection, and consequently why I didn't notice much pain there.
Now, what you really want to know...
I work out performing a wide range of exercises now. However, lately I've noticed some pain in the region again. What I've begun to do is pay much closer attention to the shoulder area, work the shoulder evenly, and be sure to work the rotator cuff muscles! I've noticed that the pain has become minimal, and I do perform heavy chest and shoulder movements. There are some exercises that seem to aggravate it, so I stay away from those. I also make sure I stretch frequently. It's been a dissapointment to feel pain again, but as I said it's manageable. The pain prior to the surgery was intense, and I don't regret having it done. If I haden't, I wouldn't be working out with near the intensiiity I am now, if at all.
You will have to weigh out the cost and benefits to you, and then make the best educated decision you can. Read up, and ask your Doctor plenty of questions.
HTH, and good luck with your decision.