Praise be to Allah the Lord of the Worlds.
Islam has forbidden whatever helps in committing sin since Allah the Almighty says, "Help ye one another in righteousness and piety, but help ye not one another in sin and rancour: fear Allah. for Allah is strict in punishment."{Al-Ma`idah, 2}. Actually, the degree of prohibition for helping others commit the sin of Riba is higher compared to other sins. Jabir said that Allah's Messenger (PBUH) cursed the accepter of interest and its payer, and one who records it, and the two witnesses, and he said: They are all equal.{Related by Muslim}.
Mostly, employees` accounts at those banks aren`t based on usurious contracts, because they have zero interest.
In conclusion, it is safer that the employer transfers the salaries of the aforementioned employees via an Islamic bank. And Allah the Almighty knows best.