Hmm...and how are Ikeda's knees doing today?
Are his knees bad because suwari waza is inherently destructive, even in small amounts, or are his knees bad because of the extreme approach he took to training? Honestly, I don't know...
I never did suwari waza for long periods of time at once, unlike the 45 minutes solid of suwari waza that Ikeda Sensei did in a Saturday morning class at a seminar over 20 years ago. My personal experience was that the video/DVD was a good source of a range of practices that I could use - for 5 minutes or so at a time - to focus on and improve various aspects of my suwari waza.
PS - For the purpose of complete clarity, I had to stop doing suwari waza about 8 to 10 years ago not because it had damaged my knees but because I have muscular dystrophy and the muscle deterioration had reached the point where I couldn't move properly anymore. At that point, doing suwari waza meant that I was moving wrong and definitely NOT doing my knees any good.