My first thought was Margot Frank & Margot is a form of Margaret.  So no, I wouldn't necassarily assume Margaret to be a Christian name.  However, I am not Jewish.  

As a Catholic, I don't associate the name Margaret as strictly Christian. If you had chosen Magdalene or Magdalena,  I would think of St. Mary Magdalene right away. But I think Margaret is pretty universal.

Unlike cames like Christian, Christopher, Dolores, Mercedes, Pilar, Rosary, etc., Margaret does not have an explicitly Christian meaning or association. There are several saints named Margaret, but they are not particularly prominent.  Margaret means pearl, and pearl names (both given and surnames) are in common use by Jews.  I grew up with two Marjories (Marjorie is a form of Margaret).  The Hebrew form  of Margaret is Margalit which may appeal to you.  I also grew up with a Gretchen, another form of Margaret.  I personally don't see any problem with giving a Jewish girl a pearl name, whether it be any form of Margaret (originally Greek) or Pearl itself.  In fact, I think Margalit, nn Maggie, would be lovely.

No, I don't. I grew up Catholic, and I don't  associate Margaret as aChristian name.

A name like Mary Margaret probably would, but because of Mary, since Mary ___ is fairly common among Catholics (or used to be, anyway). But Margaret, no.

I am Jewish and I wouldn't give it a second thought if I encountered a Jewish Margaret. In fact, I have a friend who named his daughter Elizabeth Margaret and never once did I wonder why a Jewish couple would use that name. Mary, Christ-anything, yes, but definitely not Margaret.

I don't see any issue with a Jewish Margaret, but I love Miriam's suggestion of Margalit. You could also use Magnolia as the full name, if that appeals to you. 

Well, it is for me, but I grew up in MA, where Irish Catholics were the majority, and Margaret/Maggie/Margo strike me as Irish.  So I have a very Catholic association with the name.  That said, I wouldn't really blink if I met a Jewish Maggie.  Jews are named all kinds of things these days, not just Rachel and Sarah, etc.  I wouldn't let it stop you.  Though you might consider Miriam if you like the sound of Margaret.  Or choose a Hebrew middle.  Margaret Ruth sounds lovely to me.