Why is the burden on the employee?
Unless the government interferes there is no more burden on the employee that want a part of the compensation for his work to be condoms than on the employee that want a part of his compensation to be gold coins. All they have to do is to find an employer that will agree to compensate them the way they prefer.
If Catholics don't want to follow employment law then they shouldn't start businesses. No one is holding a gun to their head.
The Roman Catholic own his business. The government don't own it. It is his. He should be free to offer to trade money (and only money) for work instead of money and condoms. An employee should be free to accept the offer, reject it or try to negotiate. A Roman Catholic employee owns his capacity for work. The government don't own it. It is his. He should be free to offer to trade his work for money (and only money) instead of money and condoms. An employer should be free to accept his offer, reject it or try to negotiate. If an employer and an employee can't agree on the conditions for a trade no trade is done. No one has forced anyone to do anything.*
By creating a law that forbids employing people without giving a part of their compensation for the work in condoms the government points a gun to all employers and potential employers heads and tell them to do it, fire all employees or risk government violence. Before Roman Catholic employers were free to not pay for contraception for their employees. After they are no longer free to not pay for contraception for their employees. The government is forcing the view that it's OK to pay for contraception on Roman Catholic employers. It is also forcing Roman Catholic employees to accept a promise of free condoms as part of their pay. You seem to believe that forcing beliefs on someone is wrong. You should therefore oppose this kind of laws.
* If any Roman Catholics reading this feel the argument is to secular please let this Protestant give you some pointers concerning what the Bible your own church agree is the Word of God (Dei Verbum) has to say about property rights: Exodus 22:1-9, 1 Kings 21:1-20, Leviticus 19:11-15, Romans 2:21, Acts 5:4