Just say no to pull ups and any other exercise that is causing you pain. Many times this is easier said than done. Clearly if you are a powerlifter and it's the squat that's causing you pain, you can't just eliminate that exercise from your program. In that scenario you have to find out what is causing the pain and remedy the issue.
Meanwhile, you can usually find alternative exercises to accomplish what you need. It seems very obvious, but I have found myself swimming upstream with this concept for decades. I really hate when my body tells me I can't do something. My mind usually fights the idea and I end up hurting myself. Sound familiar? If it does, read on, if it doesn't, congratulations, you are further along on the evolution chart than I am.
I have had this happen with many exercises through my tenure under the bar. Most recently, pull ups have been wreaking havoc on my body. Oddly, it's an exercise that I used to be able to do frequently. Now, I'm getting debilitating shoulder and thoracic pain from them. I should get it checked out, but I probably won't.
Meanwhile, I had gotten away from them for a few weeks and my back and shoulders were just to the point of being completely pain free - the impossible dream. I bet you'll never guess what exercise I went back to while in Aruba. You got it, pull ups. Jess and I found a little outdoor fitness course on the beach to train. We did a circuit of push ups, squats, and pull ups.
Perhaps you all won't be as shocked as I was, but I woke up the next morning in terrible pain. The same pain I just spent weeks fighting off. I was so mad at myself. Being in pain sucks, but being in pain while on vacation blows even worse. I'm so stupid.
I love pull ups, but seriously, do I need them? I can certainly develop my muscles and increase strength with other exercises. So this puts pull ups on a list of exercises I should no longer do. Not ironically, the older I get, the longer this list gets (or should get). Will I ever try them again? I really don't know. But do I have to? No. Hopefully the little note I left on the gym white board will serve as a good reminder.
Whether it's dips causing you shoulder pain, pushdowns causing you tendinitis, or anything else that is jacking you up. Ask yourself, "Do I really need this movement in my program?" If the answer is "No" get your brain and ego in check, your body will thank you.