What if my paper is accepted, but later my institution doesn’t allow me to publish in this journal?
Your question is the result of going against the grain. You should have looked first if your university had any rule regarding which journal to publish. This is important even now as you can re-submit to another unwanted journal by the university. 

Depending on the limited data given by yourself I suggest you  get a confirmation from the journal that your article will not be published by them. Until that time, do not send your article to another journal for review. 
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Again I assume that perhaps you wanted to fund the article through university and that is why university refuses article. Is this the case? If it is, then you should either publish without any funding from the university or follow above mentioned suggestion.