Affiliation when submitting a revised paper
Affiliation is mostly for identification. There is no formal definition requiring it to be linked to the institution in which most of the work was done. I'd suggest that you follow the advice of your director, for political reasons if no other. It may be important to the current institution to connect itself to your work. 

But there is no reason that you can't also acknowledge your former institution within the paper if they also gave you support. Add a footnote mentioning the institutions that supported the work.