The Nationalists owe their one-seat victory in 2007 to his request for a recount in the Highlands and Islands.
The initial count gave the SNP no List members, but the result was challenged by Thompson as the returning officer walked to the podium. In the end, his party won two seats, one of which went to him.
Asked whether Scotland would be in its current position if he had held his tongue, Thompson replied: "Probably not. That weekend, Jack McConnell would have been declared the winner. We'd have lost the election."
Sitting in a cafe beside Holyrood, the 64-year-old unleashes a smile: "Here we are now."
Seven years later, Thompson is the MSP for Skye, Lochaber and Badenoch and also convener of Christians for Independence (CFI).
CFI, which holds its annual general meeting this week, was set up in 2009 as an SNP conference prayer group.
Its key figures - Thompson and fellow SNP MSP John Mason - last year turned it into a cross-party organisation for selling independence to the near 50% of the population who identify themselves as Christians.
"We wanted to broaden it out, not just to include SNP people. So we put together a business plan and we submitted it to [Stagecoach founder] Brian Souter," he explained.
"Brian Souter agreed, liked our business plan and gave us £100,000, which meant we could employ David Kerr as our director."
Souter's role in CFI and the SNP, for which he is also a donor, is controversial.
The Perth-based tycoon funded a referendum in 2000, in opposition to the then Scottish Executive's policy on homosexuality in schools. Does Thompson agree with the liberal criticism of Souter's referendum?
"I don't particularly want to look back at that," he said.
"That was a position he took at the time. It doesn't affect where we are going as CFI and he has no direct role, no indirect role, no role at all, in saying what we should spend the money on."
Souter's cash is to be spent on a salary for Kerr - a former SNP candidate - and newspaper adverts for meetings, but there are no plans yet for billboards.
Thompson, who was a council worker before entering Holyrood in 2007, is what some might call a born-again Christian:
"When I got to about 14, I discovered the world and went my own way. I didn't darken the door of a church apart from funerals and weddings for about 30 years. And then God got a hold of me and pulled me back in. I've been on a journey of faith ever since."
He sees the role of CFI as ensuring the voice of Christians is heard in the referendum, and of protecting faith in any post-independence constitution, a subject the group will organise a conference on.
"We just want a fair crack of the whip and to make sure Christians aren't squeezed out of the public square," he said, adding. "There are people who would like that to happen."
"There are plenty of folk who just think that Christians shouldn't have any voice in the public square at all. There are bodies like the Secular Society, who are pushing very hard to remove people's rights in terms of conscience."
Thompson sidesteps a question on how Jesus would vote in the referendum, but claims: "The Bible doesn't support or decry independence for Scotland, you couldn't take a passage out and say 'there you are', but there are lots of references in the Bible to the nations. Immediately, that means having a nation is OK. The question then arises: where are the boundaries of your nation?"
His own politics cannot be squeezed into a political pigeonhole.
On economics, Thompson is on the centre-left and speaks passionately about trade unions and reducing poverty.
However, he is a social conservative and has no regrets about voting against equal marriage: "I'm very comfortable with civil partnerships. I didn't think it was necessary to go the next step and approve the marriage thing. I think there are dangers there."
Thompson is even more conservative on abortion and offers an anecdote about his mother, whom he says was born out of wedlock.
"If abortion was as easy as it is now, my mother would never have been born. She would have been aborted, therefore I wouldn't have been born, my brother and sister wouldn't have been born, my children wouldn't have been born, my nephews and nieces wouldn't have been born."
"It is basically used as a method of birth control. People should be a bit cleverer about birth control than having to use abortion."
"People would argue 'no, no it's not, you've got to get two doctors', but it's very, very easy to get an abortion."
On such issues, don't expect Thompson and Women for Independence to share a platform any time soon.
The CFI's presence in the Yes campaign - a largely liberal-minded coalition - is more proof if any were needed that the next three months will be anything other than dull.