Without an intent to fraudulently obtain a marriage license, there is no crime in question. Proving intent to defraud the state to obtain an illegal marriage would be a stiff burden for any prosecutor to take on, especially with a civil disobedience/protest defense available. What's more, even if such a case were miraculously successful, there are a great many avenues of appeal that would almost certainly overturn any conviction of this type.
It has always been illegal for a clerk or other official to accept knowingly false information to issue a marriage license (or other government permit or document) so, again, nothing new here except a lesser penalty for the infraction.
Indiana has not created new laws with regard to same-sex marriage and the changes to existing law do not change the legal landscape other than to lower the penalties for infractions of this law. This new concern doesn't stem from new law, but the confluence of a 1997 law criminalizing false information on a marriage application, the 2003 law banning same-sex marriage in Indiana, and the slow-moving modernization efforts, which have been ongoing for nearly a decade (and which has not rolled out to all of Indiana's 92 counties.)
What this incident actually proves is a bigger point about how these marriage bans are mean-spirited and discriminatory in addition to not being well thought out. It says a lot about the unintended consequences of such laws when two loving people, who simply want to share a life together, have to worry about potentially breaking the law just to ask to be married.
Since this blog had mentioned the story where it seemed that Indiana had taken some draconian measures against same-sex couples reminiscent of what is happening in parts of Africa, it's only fitting that the clarification also appears here.