A former Scottish National party MP has criticised the governance structure of the SNP after a fraud investigation into her business dealings was dropped, and called for an apology from Nicola Sturgeon.

Michelle Thomson was asked to resign the SNP whip in September 2015, months after being elected, when the police began examining whether her property dealings potentially involved mortgage fraud.

After a near-two year inquiry, Scotland’s Crown Office said on Tuesday there was an “absence of sufficient credible and reliable evidence” against her to proceed to prosecution.

The decision came too late for Thomson’s political career as she was blocked by the SNP from restanding as a parliamentary candidate in June’s general election.

She told the BBC that an apology from the top of the SNP would be befitting. Asked who should apologise, she said: “I would say the leader of the party. Certainly somebody very senior. Yes, I would greatly welcome that.”

Thomson said she had not wanted to resign the whip, but that the party took the decision out of her hands. “I did protest but I was kind of led to believe that if I didn’t do that gracefully things would be even worse and to be honest they were in a pretty bad state at that point,” she said. “It was not my choice and it was not my decision.”

Thomson’s fellow SNP MPs at Westminster had voted to allow the whip to be reinstated, but the party’s national executive committee overruled that call.

“I suppose what I found disturbing was that I had no opportunity whatsoever to speak directly with Nicola Sturgeon and put across some of the key points,” she said. “In other words I had no chance to put across my side of the story and I find that, to be honest, disappointing.”

A couple involved in one of the property transactions told the Sunday Mail they still felt “stung”.

Christine and Billy Troy said they had sold their Paisley flat to Thomson for £37,500 and it had been sold on for £55,000. Christine Troy, 62, told the newspaper: “I’m not happy about the whole thing. I feel she preyed on vulnerable people. We were having trouble selling, that’s why we sold to them. I wish now we hadn’t.

“I believe she should have had some form of consequence.”

Thomson said that she “would never, ever in any of my business dealings want to diddle someone” but added that if she had the chance to do the same again “I definitely wouldn’t” and apologised to “anyone who does feel aggrieved”. She also criticised the structure of the SNP, which is led by Sturgeon, Scotland’s first minister, and managed by Sturgeon’s husband, Peter Murrell, as chief executive of the party.

“It’s really important that in a large organisation you have processes that are fair, robust and transparent and I have no idea what the process was because the process seemed to be different for other people to what it was for me and I don’t think that’s fair,” she said.

“In principle I believe it’s a problem. In principle from a corporate governance point of view there is no other organisation where you have the leader married to the chief executive.”

Despite her criticisms of the leadership, Thomson said she would like to be readmitted to the party and did not rule out standing for parliament again. She also suggested she may have been treated differently if she were a man. Chris Law, another SNP MP, was investigated by police over his financial dealings but was allowed to keep the whip.

“I feel that with the current leadership, because it is the current leadership, the process appears to vary on who it is. If you think about SNP male MPs that have had difficulties, are we all being treated the same?” she said.

“How can it be that the story about me ran for two weeks, but the story about the Chilcot report [into the Iraq war] ran for two days? I think there was clearly a misogynistic element and it would appear to me at every level of politics men and women are treated differently.”

Responding to Thomson, an SNP spokesman said: “Michelle Thomson stepped down in 2015 until the investigation was concluded. She took a dignified approach while the investigation was under way and will be relieved to put this affair behind her. We wish her well for the future and will be happy to engage with her about her membership of the SNP.”