What you are suggesting may seem like the logical thing in the short term, but there will be many other women in her position who are potentially being refused an education by this decision.
You don't win by forcing her to remove her Niqab, you win by educating her. That should be the priority.
These kinds of rejectionist policies are gathering all sorts of "righteous argument" to support them but they boil down to the same thing, intolerance.
I have seen far too many cold blooded attacks on Muslim clothing throughout Europe over the last few years to believe that this case is "Genuine". What is far more likely is that it is another opportunistic attempt to undermine the faith of these people by forcing them to abandon their religious convictions.