The Rule of Thumb:
If you cannot do the exercise with good form using only your body
weight, then you shouldn't be doing the exercise at all, regardless of
Stronglifts 5x5 is a good program, but that doesn't mean it is good for you. While a starting squat of 45 might be reasonable to the average person, remember that as someone who is "extremely overweight" you are in essence squatting an extra 100-200 in body weight alone. This would be the equivalent of an average weight person starting with 145-245 in weights instead of the bare barbell at 45.
A parallel squat is a natural movement of the human body, so if you are having difficulty performing a squat then that is your body sending you a warning message that something is seriously wrong. In essence, your leg muscles are not strong enough to support your body weight in a squat, and continuing to do so will ultimately result in serious injury. If you wish to do squats, then you must either use supplementary exercises to build the leg muscles until they can support your weight (hard), or lose enough weight so your muscles have less of a load to support (easy). Those are your only two options.
I recommend re-evaluating your goals that led you to choose Stronglifts as a program. Is your goal to only gain strength? If so, modify the program to only use exercises that you can do with good form. For instance, maybe the leg press would work for you, as it mostly removes your body weight from the equation. Going this route will help build your muscles up to the point where eventually they will be able to adequately support your body weight, at which point you can attempt doing squats again. But as I said before, this route is substantially harder compared to losing weight.
If your goal is instead losing weight, being healthier, or rehabilitating your knee, then I would recommend not pursuing Stronglifts and shifting your focus to another program. While SL claims to be great for all three of these goals, that is only in the context of the average person. In your specific case, you would be far better served through a program that revolves around dieting and cardio alone. Strength training runs directly contrary to losing weight, and your body weight is currently the biggest factor contributing to your health and your weight/muscle ratio.