Jeremy Corbyn has replaced his pro-Trident shadow defence secretary, Maria Eagle, with his ally Emily Thornberry in a reshuffle designed to create a more unified shadow cabinet.

The Labour leader moved Eagle to shadow culture secretary, mostly because she disagreed with his position opposing the nuclear weapons system.

However, Corbyn decided to retain his shadow foreign secretary, Hilary Benn, after coming to an agreement on their future working.

The deal means there will be no repetition of their disagreement about the vote on bombing Syria, during which Corbyn argued against military action and Benn gave a speech in favour. All future positions on foreign policy will be directed by Corbyn, a Labour source said.

As well as replacing Eagle, Corbyn sacked his shadow culture secretary, Michael Dugher, and shadow Europe minister, Pat McFadden, for what Labour sources said were displays of “incompetence and disloyalty”. McFadden is being replaced by Pat Glass, who chairs Labour’s pro-EU group. Emma Lewell-Buck gets a promotion to shadow devolution minister.

In a statement, McFadden said he had originally accepted the post because the EU issue was of “crucial importance” with an in/out referendum looming.

“Tonight Mr Corbyn has told me he does not want me to continue to serve on his front bench, in particular because of questions I asked about terrorism and national security in the Commons statement following the Paris terrorist attacks,” McFadden said.

“It is his prerogative to decide his frontbench team and I will continue to support and work for Labour in any way I can. I hope Labour retains its strong and clear position to campaign for the United Kingdom to remain in the EU.”

Asked on BBC Radio 4’s Today programme if he thought his statement in the Commons after the Paris attacks was a reason for his dismissal, McFadden said: ”I think it’s got a lot to do with it. Certainly, when I spoke to Mr Corbyn late last night a fair few times on the phone he said that he felt that it was an attack on him and that he’d come to the conclusion because of that, and one or two other things, that I shouldn’t continue.”

McFadden added: “On this question of terrorism and our response to it, this is not just a quip or a difference of wording, this is an issue of substance.

“After the Paris attacks we’d had statements about France reaping the whirlwind of their own actions [a phrase used in a statement by the Stop the War Coalition, of which Corbyn is a long-time supporter], and every time we have a terrorist attack we have this argument that ‘what can we expect?’ That this is somehow not really the responsibility of those who carry out those attacks. I very much disagree with that view.”

McFadden, who was first made shadow Europe minister in October 2014 by Ed Miliband, added: “Me saying terrorists are entirely responsible for their own actions, that no one forces anyone to kill innocent people in Paris, to blow up the London underground, to behead innocent aid workers in Syria … He clearly interpreted that as an attack on him. You ask what is the difference between my view and his, and he’d have to explain that to you.

“We were promised when Mr Corbyn took over that there would be a new and open and more pluralist politics where people could speak their mind on things and I would hope that that would take place.”

The developments were revealed by Labour sources in the early hours of Wednesday, more than 30 hours after Corbyn began his reshuffle. The sources insisted Eagle was keen to move to the shadow culture role from defence and was happy with her shift sideways.

Corbyn had wanted to move both Eagle and Benn, but up to 10 shadow cabinet ministers threatened to resign if the shadow foreign secretary were to be moved.

Thornberry was appointed because her views on the issue of defence are felt to overlap more with Corbyn’s. It marks her return to the shadow cabinet after she was forced to resign from her role as shadow attorney general under Ed Miliband for tweeting a picture of a white van and St George’s flag, an action that was interpreted as snobbery.

Labour sources made clear that open dissent against the leader would not be tolerated in future and there would be no repeat of the situation in which Corbyn and Benn argued different positions over Syria from the front bench.

A Labour source said some shadow ministers had “got into the habit” of attacking the leadership and the reshuffle did not contradict the new politics of allowing debate.

The decision to retain Benn will disappoint some of Corbyn’s allies who had warned that the shadow foreign secretary would be at the centre of future rebellions, such as the vote over Syria, if he remained in post. One Labour MP said Benn would be a figurehead for repeated shadow cabinet rebellions if he was not removed.

It is understood there are still more shadow junior ministerial announcements to come but the shadow cabinet movements are now concluded, with 17 women and 14 men in top jobs.

Labour sources said Dugher was removed from his job over his disloyalty, including warnings against a “revenge reshuffle” and criticisms of Stop the War and Momentum, the grassroots group of Corbyn supporters.

They pointed to McFadden’s comments in the House of Commons about the Paris attacks as the reason for his sacking, suggesting they were a “coded attack” on the leader.

McFadden had asked David Cameron to reject the view that terrorist acts were always a response or a reaction to what the west did and to agree that such an approach risked infantilising terrorists when the truth was that they were adults, entirely responsible for what they do,

However, the Labour sources said it was not the only reason for moving McFadden, who had more recently warned Corbyn against conducting “a revenge reshuffle”.

In a parting swipe, Dugher said he had chosen to speak out because he was “frustrated and angry” at members of Corbyn’s team for briefing the press against other members of the shadow cabinet in a way that amounted to a “terrible trashing of people’s reputations”.

“I thought that was hugely damaging,” he said. “I thought it was really unfair on those people.”

Shadow cabinet ministers including the deputy Labour leader, Tom Watson, and the shadow home secretary, Andy Burnham, defended Dugher, saying he was a strong campaigner who was vital for winning back working class Labour support in the north of England.