The word "conceive" has a few meanings, and one of them means "to become pregnant". For example: "She conceived her first child at the age of 49."
Therefore, your sentence means "Senora Begum was raped last year by Myanmar security forces and (became pregnant with) a baby through...."
Just as a side discussion, "conceive" can also mean to think of an idea or to imagine something. So, "conceive a baby" does not mean "imagine a baby" or "think of an idea regarding a baby".
I hope this helps.