It was the moment the new, more tribal phase of the Coalition became very public.

When Nick Clegg announced the Government's plans for an elected House of Lords on Tuesday, Tory MPs spent 70 minutes pouring scorn on the Deputy Prime Minister, sniggering behind his back on the Commons green benches like naughty schoolboys. You would never have guessed he was speaking for the Government. Labour MPs joined in the game – even though, like the Liberal Democrats, their party supports a 100 per cent elected second chamber.

There was a similar unholy alliance the next day when Kenneth Clarke made his foolish remarks in a BBC Radio 5 Live interview about some rapes being more serious than others. The nasty party within the Conservative Party sensed blood after Ed Miliband elevated the story by demanding Mr Clarke's sacking at Prime Minister's Questions.

Many Tory MPs dislike the Justice Secretary's allegedly "soft" approach to sentencing and seized their opportunity to press for both Mr Clarke and his policy to be dropped.

Again, Labour broadly supported the minister's approach but could not resist the temptation to score easy political points. If Mr Cameron had thrown Mr Clarke overboard to the Tory sharks, his sensible approach to prison would have been junked too. The man dubbed by fellow ministers as "the sixth Liberal Democrat in the Cabinet" might have been replaced by a Tory hardliner.

It was the accident-prone Crispin Blunt, a junior justice minister, who sparked the affair. Answering Commons questions on Tuesday, he unwisely chose rape as his example, while defending plans to raise from a third to a half the "discount" on sentences for people who plead guilty soon after being charged. If he had cited burglary, the furore would never have happened. Mr Blunt's remarks resulted in a Daily Mail front page headline saying: "Soft justice for rapists", which provoked the questions to Mr Clarke during that fateful interview.

It would be a pity if his policy were abandoned because of the row. More than two in three crown court cases end in a guilty plea. In 2009, more than 10,000 defendants decided to admit guilt at the door of the court. The delays waste time and money and often add to the anguish of victims.

Mr Clarke had to postpone next week's launch of his higher "discount" scheme, which would reduce the prison population by 3,400 and save £130m a year. As it comes under attack from Tory MPs and right-wing newspapers, those savings may yet prove his trump card. A decision is now expected when the Justice Secretary unveils his Criminal Justice Bill next month. Rape and other serious offences may be excluded but the scheme is likely to survive. "There's no money," one minister said.

There are signs Mr Cameron is losing patience with Mr Clarke. Number 10 aides are nervous that his "prison isn't working" mantra sends a signal to the voters that the Tories are "soft" on crime. A poll funded by Lord Ashcroft, the party's former deputy chairman, found that 79 per cent of people who considered but stopped short of voting Tory last year said crime was an important issue for them. But only 43 per cent believed it was an important issue for the Conservatives. Tory MPs, delighted that Mr Cameron discovered his "inner Conservative" during the AV referendum, warn that the Tories must protect themselves against Labour raids on law and order, immigration and Europe. "The Conservatives should be aware of this potential strategy and ensure we are not outmanoeuvred," said Mark Pritchard, secretary of the 1922 Committee.

Mr Cameron is likely to reshuffle his Cabinet next spring and Mr Blunt will probably depart and Mr Clarke might be offered Leader of the Commons to prise him out of a law and order post. But after 40 years in frontline politics, he might decide to call it a day. That would be a sad end for the best leader the Conservative Party never had because it could not stomach his pro-European views.

He may sometimes irritate fellow ministers by starting sentences with "when I was Home Secretary", but he has held most big Cabinet jobs and played an important role in making the Tories electable when he returned to the Shadow Cabinet in 2009. They needed his experience and gravitas then. Although he had a bad day at the office on Wednesday, they still need him now.