Some poses will always be problematic to some people, but it seems to me that focusing on foot loop and inner spiraling the thighs really improves knee safety. This language might be unique to Anusara and/or Iyengar, but I think any style of yoga has the same concepts of alignment? My teacher always makes sure we engage the feet, and sit on whatever we need to to keep the knees below the hips, in sukhasana.
http://www.doyoga.com/update_article...ted_update.pdf
http://www.yogatic.com/yoga/principles-of-alignment/
I know for me that I've had to work a LOT on foot strength and flexibility. It's coming, little by little. It's been so exciting to me to start seeing some movement in my tarsal-metatarsal joints, that had been completely locked. :)
It's a fine line, too - especially with your history of pushing too far - but for me, yoga brings blood, lymph and healing to injured areas like no other workout does. There's a kind of ouch I can tell is good, but there's definitely an ouch to avoid, too, and you're probably best avoiding anything that hurts.