There's no good without bad. I consider freedom of religion (along with its vitally necessary companion, separation of church and state) to be a basic human right. It is, therefore, "good."
But just like freedom of speech, another basic human right, there are disadvantages. Ironically, freeing speech requires one to give up certain freedoms--the freedom not to be pestered with stupidity and inanity come to mind. If you grant everyone free speech, you have to be prepared to hear what they say even if it turns your stomach.
Religions like JWs are the "bad" side of freedom of religion. There will always be people willing to use religion to control others and unfortunately, like porn, it is something that can't be quantified legislatively. You may "know it when you see it," but if you can't completely define it and isolate it from other "fair uses" of freedom of religion, you can't legislate against it.
I'm willing to take little details like my wasted childhood and, yes, even children dying for lack of blood transfusions or other refusal-of-care issues from other whacko nutjob holy-roller fundie religions, in order to have freedom of religion in the modern world. They are part of the bad that comes along with the good.
u_b