The best way I can analogize RFRA, generally, and specifically as it applies to Indiana is to think of RFRA as a tool.

So if you have a hammer and some saws, you could do something productive, like build a house, if thats what your intent is. Or you could wield it to do something unproductive and mean-spirited, say to injure people.

The First edition of RFRA in 1993 was to actually protect religious freedom of Native Americans to use peyote. Later the supreme court held that federal RFRA doesnt apply to states, so a bunch of other states (many in the pre-gay marriage era) enacted state RFRA laws so that there are state protections for folks to exercise religious freedom and practice without government interference.

The real problem with Indiana's RFRA isn't the law itself, (remember its just a hammer or some saws), but the problem is the intent with which it was passed, and the fact that Indiana doesn't have state law that considers LGBT people as a protected class for discrimination purposes.

So given that the Mike Pence and the Indiana legislature tried to enact RFRA on the hush hush, that he's gone on the Sunday talk shows and made clear that there is no intent to protect LGBT folks with other legislation means that its pretty clear the Indiana RFRA is meant to be discriminatory toward gay people. There's just no other way around it.

The only fix is for Indiana to enact a specific anti-discrimination law that covers LGBT people. The damage is done in regards to the fact that Indiana republicans just outed themselves as bigots (as if there was any doubt), but theres still time to fix things.