If you are eligible to pursue B.Com after 12th in a Science stream, you have surpassed the biggest hurdle. The moment you complete your Graduation, your subjects in 12th become irrelevant because your future now depends on the next step you take after B.Com and the eligibility criteria depends on your Bachelor's degree. You can join CA Intermediate through Direct entry scheme. You can study M.Com, MBA so on and so forth on the basis of your B.Com degree. Even if you want to apply for Government exams like IBPS or UPSC, they need your Bachelor's degree and not what you studied in your 12th. So there will be no issues whatsoever even if you complete your B.Com after 12th in Science stream.