How could (and why should) the HHS mandate be held unconstitutional under Smith?

I oppose the HHS contraceptive mandate, but I admit to being confused (and a little troubled) by the argument that, under Smith, legislative exceptions make it more likely that a statute is unconstitutional.  I understand that there are exceptions built into the rule of Smith, though I don't know the case law well enough to have a good sense of how they play out in practice.  I'm having a hard time seeing how the exceptions -- especially to the extent that those exceptions are triggered by the existence of exceptions in the legislation at issue -- could stretch to encompass the HHS mandate.  Marc writes:

The HHS mandate contains many, many exceptions: exceptions for grandfathered organizations;  hardship exceptions of various kinds (I believe, but am not certain); exceptions based on the number of employees the organization has; and perhaps others.  There is a quite plausible claim to be made (it has been made already, several times, in pending litigation) that these exceptions can ground a claim that the government has violated the Constitution. 

If the legislative exception itself calls into question the general applicability that is at the heart of the Smith requirements -- i.e., the exceptions suggest that certain categories of practices are being targeted for reasons unrelated to the objectives of the underlying rule -- I can see why Smith wouldn't apply.  But if the exceptions are driven by the objectives of the underlying rule, why would that take us outside of Smith's scope?  Exceptions based on the number of employees or on the fact that the organization serves members of the sponsoring religious group appear to be related to the underlying rule's objective.  There is no suggestion that HHS is picking and choosing the practices and groups that it prefers through the exceptions to the mandate.

Alternatively, if the exceptions are taken to be evidence that the government interest at stake is not all that compelling since the government is willing to give ground on certain aspects of the legislation's enforcement, doesn't that simply take us back to the pre-Smith balancing approach, from which Smith was a dramatic departure? 

More broadly, to the extent that the presence of exceptions is enough to call the Smith rule's applicability into question, isn't the easy legislative response to stop granting exceptions?  Is that result good for anyone?