This would be an incorrect statement and you're basing it on a bill Pence signed into law. http://www.in.gov/legislative/...
This bill reclassified various criminal offenses, including "providing false information to a clerk of the circuit court" from a Class D to Level 6 felony. It didn't create any new crimes or make the crime in question any harsher.
The "crime" of applying for marriage licenses came about from the fact that the online method of applying for marriage licenses did not permit you to select male-male or female-female as a combination as the website was created in accordance with the Indiana law that made marriage between people of the same gender illegal. Thus you had to select one spouse as male and one as female. No one has ever been jailed or even prosecuted for doing such a thing so that claim falls short as well. This crime is not specific to homosexual couples as it is with regard to giving the court false information. A couple that submitted the male spouse as female and the female spouse as male would also be equally guilty of the crime. Perhaps the more damning point against your claim that "A bigot who once made it a criminal offense for gays to apply for marriage licenses" is that homosexual couples could still apply for marriage licenses without breaking the law in question by using the paper form and crossing out the male or female section and writing in the appropriate gender.
But hey, whatever, thanks for perpetuating a falsehood to push your own narrative and belief.