The cost to actually send the money to the employee direct deposit is $0.35 per transaction. That's what the payroll service pays, and what you'd pay if you did it directly. That is what ACH charges. It is a cheap system. That's why places are more than happy to have bills paid via ACH. When they do an ACH deduction, they pay the fee (the initiator pays), but it is so very cheap in terms of getting money. Much less than a CC.
In terms of an actual check, it varies but is generally in the range of $0.75-$1 when you count the cost of the check stock, printing, envelope, and postage fees. Perhaps a bit more if you factor in labour (depending on how automated the system is).
Neither system costs an employer much. Checks cost the bank somewhat more to deal with, though they have automated that to a large degree, but ACH costs them nothing (when they receive). The sender pays a small transaction fee and that's it. ACH is cheap on purpose because it can be, and is, used for massive volume and thus does well.
No matter how you look at it, it doesn't cost much. The costs are mostly in the other services, as you of course notice from the cost of your payroll service that does all the other work for you (my folks used a payroll service when they ran their business for the same reason).
Still a trivial cost as compared to all the others, as you point out. $15 is trivial shit compared to the other costs of having an employee, even a minimum wage one.