Lots of pain and loose motion on periods

My periods are regular, sometimes there will be 3-4 days, but it happens every month without a miss. Initially I had no issues during periods, later on I started getting pain in first day of period. After few months, I started getting loose motion and the pain is horrible. I can't go anywhere because of this on first day of my periods. From last one year, it started paining on 2nd day as well. Sometimes I even get fever due to pain. From last 2 months I am having pain on 3rd day as well. The pain is less compared to first day, but I do have pain. As the days pass I'm seeing new symptoms during periods. My gynaecologist asked me to do scanning to determine if there is a cist. But reports are normal. She is saying there might be minor cist, which will not get detected in scan. Hence she gave me birth control pills and asked me to take it from the day period starts to next 21 days without fail. I'm scared about it. Does it have any side effects. Is it ok to take birth control pills?