Judge Richard Young, a Democrat appointed to the bench by former Gov. Evan Bayh, initially sided with the governor's argument, deciding that the broad power was not enough to show he should be a defendant.
But Young determined last Tuesday that the governor undercut that argument by issuing a pair of memos earlier this summer to state staff dictating precisely how to enforce the state's marriage law, as confusion grew over a series of rulings overturning the same-sex marriage ban.
"Since that time, the Governor issued memoranda, through his attorney, and did what he claimed he could not do by directing executive agencies on how to proceed in enforcing the law," Young wrote. "In light of this bold misrepresentation, the court must now revisit the issue."
It was a surprising rebuke for Pence, who is eyeing a run at the White House in 2016 and has worked his Washington connections to stay visible among a wide-open field of contenders and would-be candidates.
Asked Friday on C-SPAN "Newsmakers" about the rebuke from Young and whether he, if chosen as a vice presidential candidate, could support a presidential contender who supports gay marriage, Pence danced around the question, adhering closely to the same messaging he has used on the issue since becoming governor.
"I support traditional marriage and will always hold that view, and I've long believed that issues of this nature are best decided by the people and not the courts," he said.
But he then added, "while my views are what they are, I want Hoosiers to know we'll uphold the rule of law."
It's a far cry from the firebrand who had many in the Republican party base swooning over a possible presidential run in 2012.
The two legislative agendas he has pushed have been somewhat amorphous, changing as his staff felt out the political pulse of the Statehouse. But the few constants have mostly been education and tax issues - hardly contentious issues like abortion and gay marriage.
Heading into the legislative battle earlier this year over whether the state's ban should be added to the constitution, there was some question whether Pence would support the ban. He had consistently stated he supported "traditional marriage" through 2013, but had yet to say whether he would place himself.
He appeared to stake a claim on the issue by including his support in his 2014 State of the State address, using valuable space in his annual speech to support putting the ban up to vote on the 2014 ballot on whether it should be added to the state constitution.
But as that effort foundered first in the Indiana House and later in the Senate, Pence kept his distance, choosing not to press lawmakers behind the scenes or publicly lobby the issue.
For a little more than a month, the issue slumbered. But it quickly jumped back to the fore with a slew of lawsuits that were filed started in March challenging the state ban - the first Indiana had seen.
As those lawsuits now wind their way through the courts, Pence continues to garner national attention, the issue of gay marriage is likely to cause a few more bumps in his road.