I am not a teacher.
I think you can use mixed tenses in your sentence. What's important is the idea you're trying to convey. As you said, if you use the simple past tense in the second part of you sentence, the meaning will be materially altered.
I would think the first sentence implies the person in question is on leave all day today. The second sentence suggests that the person in question certainly was on leave earlier today but now it has already finished.
Student or Learner