Trudeau also said he won't allow candidates carrying leadership race debt to run in 2015.
Earlier this month, Innes was told she couldn't run for the federal Liberal nomination in Toronto's Trinity-Spadina riding, where New Democrat MP Olivia Chow resigned to run for mayor.
Innes said the dispute was over her refusal to sign an agreement committing her to run in the newly created Spadina-Fort York riding in 2015.
Party officials, including Trudeau, said she was denied a chance to run because her husband was allegedly bullying young volunteers.
"My promise around open nominations is only kept if the nominations are truly open," Trudeau said outside the House of Commons following the party's weekly caucus meeting.
"And if someone is engaging in intimidation tactics and bullying young volunteers, that's simply something that is unacceptable and I will not stand for on my watch at the Liberal Party of Canada."
No to leadership debts
Trudeau said the party had "many, many meetings with [Innes] and her campaign team over the weeks leading up to this decision."
"Those are the kinds of behaviours that led us to being at 36 seats in the House of Commons.... Warnings were not heeded, which led us to this unfortunate situation. But it actually gives us an opportunity to actually have an open nomination in Trinity-Spadina," he said.
Trudeau also said it's a flat-out "no" to possible candidates for 2015 who carry leadership debt from past races.
That could affect David Bertschi and George Takach, who owed $155,025 and $136,000 from their runs at the 2013 leadership as of last November's reports to Elections Canada. Eliminating Bertschi as a candidate for the nomination could serve to smooth the road for Andrew Leslie, the former head of the Canadian army, to represent the Liberals in Ottawa-Orleans.
It could also affect current MPs Marc Garneau and Hedy Fry. Fry still owes $42,000 from her 2006 leadership run.
"We've seen over the past years how our political opponents have certainly made a lot of hay out of the difficulties with the change of rules in repaying certain leadership debts. And that's certainly something I've committed to, going into 2015, that we will not have in that election any nominated candidates with leadership debts outstanding," Trudeau said, noting candidates have until November to have "amply" repaid their loans.
Bertschi last week sent a note to supporters in an attempt to raise $25,000 in 10 days to help pay off his debt. He estimated earlier this month that he owed between $110,000 and $120,000.
That's not Bertschi's only hurdle, however. He also went over the $100,000 debt cap that the party set for the 2013 race.
Trudeau said that's a "discussion within the party."
"And that is something that the green-light committee is seized with," he said.