The Boundaries of Toleration
Hall clearly endorses religious exemptions more so than Rakove does. That's the point of the review. However, figuring out how the founding fathers/First Amendment ought to apply is complex. Like Hall, I tend to generously support religious exemptions. Though I think Justice Scalia in Employment Division v. Smith got it right that the Free Exercise Clause of the First Amendment doesn't require such.
That is, to the extent that these exemptions are legitimate, they are as creatures of legislatures and state constitutions.
Further, scholars such as Marci Hamilton, Philip Hamburger and Phillip Munoz have demonstrated that such is the correct originalist understanding of religious liberty. True, America's founders did support giving exceptions and accommodations from the secular law that might burden religious practice. But did so more as a privilege that could be taken away.
(I understand this point is quite contentious in some scholarly circles; but at the moment I would kick the can to the above mentioned three scholars and can link to some of their arguments in the comment section if any readers so desire.)