There is nothing about spinal bifida in and of itself that would absolutely prevent you from having a surgery on your knee. In fact, people with chronic musculoskeletal problems from spinal bifida, cerebral palsy, and other life-long neurological conditions are often among the patients who benefit most, in turns of quality of life and improvement in function, from orthopedic surgical procedures.
Therefore, what I would suggest is that you go ahead and meet with the orthopedic surgeon
who has been recommended to you by your primary doctors. That surgeon will be able to perform an overall evaluation of your situation and of your specific injury
and make recommendations about whether or not surgery is a good option for you.
Sometimes, ACL injuries settle down with time and do not require surgery, depending on how severe the tear is and how unstable the knee is afterwards. I think from your question that you say it has been only 2-3 weeks since your injury; if that is the case, there is still plenty of time to allow the inflammation to go down and healing to occur. Therefore, the orthopedic doctor
may recommend rest and physical therapy for a while instead of surgery.