I know this is a fools errand, but...
You seem to have a funny understanding of the meaning (and spelling) of the word "exactly." It is not remotely the same.
Wow, you got me. That typo you caught really destroyed the argument.
Do you think that Hobby Lobby has gone snooping into their employees' private lives and has docked their pay or even fired them for "immoral" behavior?
Don't you? Hobby Lobby did, in fact, root through every employees insurance plan, made simple because Hobby Lobby arranged the insurance plans in question. Whether Hobby Lobby pays for a plan on the employees behalf, or pays the employee who, in turn, pays for a plan, the simple fact is: The insurance plan is owned completely by the employee.
If this is, in fact, a moral position for Hobby Lobby, why wouldn't they evaluate employee plans (as they are now) to ensure that Hobby Lobby money is not [eventually] paying for services of which they disapprove?
The fact that you find it unthinkable and nonsensical to think Hobby Lobby would evaluate each employees insurance plan, when that is in fact what they are doing, leaves you some mental gymnastics to perform.
The employees can do anything they want with their property (which includes their compensation after they have earned it) and their bodies, and if Hobby Lobby didn't agree to that, I doubt it would be a viable business.
Your doubts aside, Hobby Lobby *IS* meddling in the employees health insurance.
Hobby Lobby and the employees can agree to any compensation package within the law. It doesn't even have to include health benefits at all, although thanks to Obamacare, Hobby Lobby will now have to pay a penalty to the government if it doesn't offer a particular package of benefits.
Employers do have the option of offering compensation packages that include only the minimum legal requirements. Most employers realize that by offering the minimum, they don't get the level of employee or commitment necessary for a competitive business. The key point being, the specific health coverage being offered by Hobby Lobby was below the minimum level, hence the court case and the resulting bad decision.
Note also who is the one upsetting the status quo. The RFRA was designed to protect the status quo for religious freedom. If the government wants to upset that status quo, it needs to have a compelling reason, and it needs to do so in the least restrictive way possible. All that SCOTUS has said is that the government failed to meet that burden in this case.
Oddly, it seems the SCOTUS made this awful decision because ACA allowed non-profit religious enterprises a less objectionable (to them) path. The court claims that since such a path was offered elsewhere, it could be offered here. The Takeaway is this: Don't compromise. The ACA, by compromising with religious organizations, undermined their own case. ACA would not have lost if they didn't make this compromise.