There is nothing wrong with working in the transfer company mentioned, even though it belongs to the riba-based bank. Working for it is like working for one who deals in riba, which is permissible so long as the work is permissible and does not help him in doing anything haraam.
See the answer to question no. 82617.
There is nothing wrong with taking payment for making a transfer and moving money from one bank to another.
See the answer to question no. 87656
Moving to the Islamic department which is administratively and financially separate is better and is preferable, so hasten to do that.
We ask Allah to help guide us and you.
And Allah knows best.
Reproduced from Islam QA