Disclosing work affiliation in journal paper
Since you have a contract with the company already assigning all IP rights to them, the affiliation should be the company. Or, perhaps, the company as well as the university. 

But a better solution would be to ask a legal officer at the bank what is appropriate here. They can probably dictate what you say, I think, but might agree to let it be the university, depending on the contents of the paper. 

Without such an agreement, your affiliation in this case would be "Independent Researcher" or your university. Probably the university would best in this case. The research was done as a student there, not as an employee of a company. The company would be irrelevant. But the signed employment agreement has changed that. 



But some advice to others, though it won't help you. If you are already a scholar (or student) and want to take a job with such restrictions, try to work out at the time of hiring any exceptions that are possible for work related to your degree. You may have a bit of leverage here if they really want to hire you. 

And, if you are employed under such a restriction and want to take up a degree, try to work out before you start how your academic work will be considered. In this case, you have less leverage, I think, unless the company can find some other value in your work than in claiming it.