Those are not equivalent.

The difference is that a prayer room is for actual, you know, believers, to perform a religious ritual of their actual, current, religious belief. It is a mini mosque, temple, church, etc.

The crucifix in the Quebec N.A. is an historical artefact reflective of Quebec's cultural heritage, which does not reflect current religious beliefs or rituals of Quebecers any more than having the fleur-de-lys on the flag represents current belief in loyalty to the King of France.

Insisting on destroying  traces of one's religious past in the name of current secularism should be as abhorrent as the destruction of monuments of past religions by ISIS, or France destroying Notre Dame Cathedral or Chartres in the name of secularism. Ironically, Catholicism is a crucial part of the culture of Quebec, because that is what people rebelled against. 

I personally don't care whether it stays or goes, but I object to the mischaracterization of what it represents.