The minimum educational qualification needed for Neet exam is 10 + 2 passed with a minimum aggregate of 50% in PCB. Since your aggregate is 49% which is less than 50%, which means that you do not satisfy the eligibility criteria. So ,you cannot apply for Neet by  HSC because there is no compromise in eligibility criteria for NEET. 

But i didn't get what you want to say by qualifying B.sc since B.sc is a graduate level degree and no matters you do which degree , your marks of class 10+2 will only be considered.

Hope you get it!