The knives are out for Boris Johnson. With the controversy over his comments on women who wear the burqa into its fourth day, Brandon Lewis, the Conservative chairman, has launched a disciplinary probe into whether Johnson breached the party’s code of conduct.

The former foreign secretary has already refused to heed a call by Lewis to apologise for the comments. That demand – later echoed by Theresa May – now looks like the opening salvo in what will inevitably be a protracted civil war: CCHQ and the party leadership vs. Johnson.

As far as the probe itself goes, the question of how Johnson will be investigated is secondary to the question of why. Tory MPs say other agendas are at play, none of them particularly noble. (Most between its ideological poles describe his language as idiotic or clumsy, rather than racist.)

The first is the party leadership’s desire to neutralise its growing Islamophobia problem. Labour sources are briefing that by investigating Johnson, the Tories have effectively put themselves on trial: “Either Boris is guilty or the Tories condone Islamophobia.”

That they have speaks to the obvious interest both parties have in the process: for the Conservatives, botching or avoiding action against Johnson means making hay out of their opponent’s woes on anti-Semitism is much harder. Doing so, even belatedly, at least allows Lewis to argue that his party is more serious than Labour.

The second motivation is factional. Here there is the potential for an explosion. There is a sense among some Tories that the investigation is unfair. One cites Guido Fawkes's list of other MPs to have criticised the burqa without political consequence. But still CCHQ has briefed – and surely not with a straight face – that the decision to investigate Johnson “is not personal” and “has nothing to do with Brexit”.

They instead claim that “it is simply the same rules that apply to everyone in the party”. Nobody is buying that, not least Conservative MPs, and it is impossible to give that line any credence at all if you’re reading it on the front page of George Osborne’s Evening Standard as an exclusive.

If the party's insistences are true, where was the investigation over Michael Fabricant MP, who last month tweeted a picture of Sadiq Khan being mounted by an inflatable pig? There wasn’t one, and there won’t be one, because the political gain from clobbering and discrediting a backbencher like Fabricant with a costly disciplinary probe would be non-existent.

The question the Conservative leadership must now consider is whether the political cost they will pay for disciplining Johnson will be worth it. His noisiest defenders in the press have been exactly the sort of Eurosceptic backbenchers who will be prepared to take a kamikaze approach to key Brexit votes should the government refuse to yield to their demands. MPs wearily say they have already had complaints from members, who are already apopletic over Brexit.

Suspending Johnson from the whip would preclude a leadership challenge. Disciplining him for racism makes the prospect of joining one less attractive. But if the action provoked even a small-scale mutiny, the costs to the government could well be fatal. Whatever the outcome, it might prove impossible for Lewis to win.