Now, if she doesn't worship Mara, why did she keep it/put it there in the first place?
My hunch:
I'm inclined to believe that it was a part of the original structure before Valerica and Harkon moved in. Since Mara is the goddess that binds marriage, makes sense that it was in the chapel.
It's also entirely possible that they moved in prior to becoming vampire lords.
I don't remember anything about her building that part of the castle, but she did plant ('build") and maintain the garden of the courtyard. It seems reasonable that if they were there prior to becoming vamps that she would have toppled the statue afterward in reverance to Molag Bal. If there moved in after becoming vamps then they might have done the same thing.
It could also have been Harkon that toppled it. Seems to me that Valerica (even as a vamp) would have appreciated art and beauty. If that area reminded him of her I'd think that Harkon would have torn the place apart before sealing it off.