Although the immediate reaction naturally focuses on access to contraception, the decision does throw a spotlight on the more general problems of implementing the RFRA as amended by the RLUIPA.
Alito's opinion for the majority stated that "the scope of RLUIPA shows that Congress was confident of the ability of the federal courts to weed out insincere claims." This view may herald a new wave of court decisions examining a litigant's asserted religious beliefs and giving them a thumbs up or thumbs down. Traditionally, courts have resisted plunging into that thicket. Of course, activist judges like the current majority have no problem taking on that role. One can assume that adherents of mainstream Christian denominations will always win and other people will often lose.
In some cases, of course, the sincerity of the asserted belief is clear. You raise a good example concerning polygamy. At least one breakaway Mormon sect have continued to preach and practice it even when that meant fighting both the law and the much larger "regular" LDS church. That decades-long history is good evidence of sincerity. In those instances, the activist judges will have little to go on except the very thing they have always criticized most harshly when accusing liberals of activism. They will rule based on personal preference. Those five don't feel comfortable with contraception but they do support strict monogamy (even if it turns into serial polygamy). Therefore, opponents of birth control (and, down the road, perhaps opponents of racial integration and opponents of environmental regulation) will be granted exemptions from the law, but people who want to engage in polygamy or use drugs in religious rituals can forget about it.
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- In any way, shape or form.