If I get hurt whether that's during BMT or SW prep, I was wondering if that would affect my chances of getting into A&S or if that would disqualify me from the PJ route?

If you get hurt then the severity of your injury will determine your ability to stay in the pipeline. If you have an injury that will take over 60 days to heal then you will most likely be reclassified. If it is under then you have a good chance of being recycled given that you have earned it of course.