I've been doing sronglifts 5x5 off and on for about a year and a half. I've had to stop for a quite some time due to a knee injury (bad form) I've worked on it though and I think Ive fixed it. If my knee gets hurt again I will have to put the squats and likely deadlifts on hold. I'd like to keep doing the other exercises but I'm wondering if I will still make gains with the other exercises while my knee is healing?
Yes, you will continue to make gains on the other exercises if you're diet is on point. Although, if you're not squatting and deadlifting, you progress and gains will slow down. Squatting more than deadlifting initiates quite the hormonal response in your body as far as testosterone and growth hormone.
Since you're coming back from injury, I suggest you get your form checked by a decent coach/pt (one who specialises in strength/lifting), maybe also see a physio.
You will still make gains with the other exercises, but the program works best when followed as written.
I've been doing Stronglifts myself, and started to feel funny in the knees as my squats went above 120kg - I found knee sleeves have really helped, but we're different people under different circumstances. See a professional.