However, employers pay a large portion of the employee's health insurance. As the employer has a financial stake in it,
No, they don't. The health insurance, as already stated, is part of employees compensation. As such, the employer has no financial stake whatsoever in it. It does not belong the them, it belongs to the employee.
The company decides which insurance to offer, and pays a portion to the insurance company (my company spends over a hundred bucks per month on top of my own premium). The same insurance plans are offered to all employees in the company working at least 30 hours per week (or whatever ObamaCare requires). As the company is subsidizing a portion, the company can dictate which plans to offer. There is no discrimination. The company pays the same amount per employee with the same plan. If an employee wants coverage for something not covered by the company's plan, they can get supplemental insurance.
they should be able to pay for a plan that does not cover contraceptives; if the employee wishes to buy supplemental insurance for this, more power to them.
"More power to them" would in practice require separating healthcare from employment entirely, which in turn means a completely publicly-funded healthcare system. Until one is in place, the employee should not be penalized for not sharing their employers religious convictions, which is what having to take another insurance amounts to.
How is the employee penalized? He is getting the same exact company provided insurance as everyone else.
Let me put this into another context. Let's say that you belong to an HOA which subsidizes basic cable tv and internet to all members. If you want more channels, or a faster connection, you must open your own contract with the cable company and / or ISP. No discrimination is implied just because someone must supplement what is subsidized.