And sure, if you want to play sports on the weekend that's great. See how you feel. If it starts to affect your weight training, then you will have to evaluate it. If you don't care how fast you will make progress in your lifts, and you'd like to play some sports, there's obviously nothing wrong with that. Just understand that a program like Bill Starr's 5x5 is really a program for intermediate lifters, perhaps not intended for people who want to do other activities as well.
Then babies need to fire their personal trainers:
http://personaltrainerbath.com/wp-content/uploads/2009/12/BA...
http://www.malvernstrength.com/.a/6a00e553cfae8a88340120a4cb...
http://2.bp.blogspot.com/_X0yQkonFwHQ/SeINrYNoy9I/AAAAAAAAAU...
Saying squats are bad for your knees doesn't really mean anything, and I doubt your orthos would actually know offhand. If you have a question, go look up the relevant studies from the academic literature, and then ask if you don't understand something.
Don't you feel your heart pounding after a heavy set of five squats? I'd say that's adequate for "heart health."
If you're worried about staying "fit," you might consider adding in one conditioning day of pushing a sled or running sprints. 5x5 is a lot of volume, though, so I'd be careful with adding in anything extra.