All Perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger. We ask Allaah to exalt his mention as that of his family and all his companions.
Working in usury-based banks, particularly in the loan department, is forbidden for the generality of the narration in which the Prophet said: "Allaah has cursed the one who consumes Ribaa (i.e. usury or interest), the one who gives it to others, the one who writes it down and the one who witnesses it." [Muslim]
As clearly stated in this narration the one who writes usury-based contracts or witnesses such contracts, is included in that warning. Thus, in principle, prohibition is the ruling of working in usury-based banks. There is no exception from this ruling unless there is a sound basis that necessities it.
As for what the questioner mentioned; it is not a factor that should be taken into consideration except if we know with certainty or high probability, which is something hard to prove, that his absence from that position will cause considerable harm to Muslims.
Therefore, you must give up this work before death comes to you suddenly while you are in a war against Allaah (in the form of dealing with Ribaa).
Allaah Knows best.