Both are not correct. The verb "wishes" in the main clause requires a conditional or subjunctive form in the "that" clause:
12d': She wishes (that) it would stop raining!
She is wishing for a situation that is contrary to current fact.
Here are some examples that would make the other choices work:
12a': She hopes (that) it stops raining soon!
12b': She hopes (that) it will stop raining!
12c': She is glad (that) it (has) stopped raining!
I hope this was helpful.