Doc says stop running....

Sorry about your knees. Mine have taken a similar pounding. Had my first operation 30+ years ago and have gotten to the point where there is no more articular cartilage in the left knee and a little in the right. My orthopedic friends have essentially said that the damage is done, and an eventual knee replacement is inevitable, so they have recommended doing whatever I can do and being limited only by pain.
That said, there are a lot of things you can do to prolong your triathlon career. Quad strengthening is imperative - I like the nautilus type leg extension machine - I find squats way to stressful. I also find that if I plan a run, a short spin on the trainer before will loosen up the joint and decrease the pain. Deep water running is a great way to work on form and gain aerobic fitness without impact. Without opening a can of worms, I will say that the science behind supplements and synvisc/euflexxa injections is at best equivocal. If it works for you, go for it. It does not work for me but I take my glucosamine/chondroitin everyday anyway. I have also had synvisc injection series before IMF 2005. I think the steroid/lidocaine injection helped more, YMMV. If you use nonsteroidals like ibuprofen on race day, be careful to use them during training as well. I also got some knee wraps that the orthos give post-replacement patients and find them a much easier way to ice at night. I used to marvel at the old guys zipping along with their horrendous varus knee deformities til someone told me I had become one of them. I've come to grips with the concept that I enjoy triathlon so much that I'll go til I can't do it any more, then think about aquavelo type trainig.
Hope that helps.