If the knee issue is stemming from the foot being allowed to toe-in or out due to bad cleat alignment, then yeah, it would help.

If the problem is in the way the foot is making contact with the pedal (a varus or valgus abnormality), then moving the clips won't make much difference. In that case, you'd need a forefoot wedge to help align the leg. From what I've read, it's those kind of issues that can generate knee pain under load. Wedges and arch support can also help people whose tibia curve slightly (usually outward from the ankle--like my right side).

Then there are issues with the hips and pelvis: flexibility, muscle imbalances, alignment etc.