While filing any criminal case(498a/DV) against a Govt employee, immediatly he can be suspended from his regular service. that does not mean he will loose the job. But if he will convicted by the court then offcourse that will happened.
Legal separation can not avoid the involvment of family member from harrasment of such case like 498a.
Even he stayed with you only for one day, that also be enough to be involve himself into the litigation. When you are anticipating about the 498a case, first start to behave with you spouce very carefully. try to collect all evidence to be prove yourself as innocent. Record all conversation over telephone. Your thinking should be crooked and in all circumstances you should be very polite. Your brother may get transfer and write a letter to the admin/personal deptt to inform the actual fact in brief. Discuss with a Good Lawyer and first you should know the law(498a/DV) in details. Best of luck