The health secretary has told the trust at the centre of a hospital bug investigation to withhold any severance pay from its former chief executive.
The commission found countless examples of dirt
Rose Gibb of Maidstone and Tunbridge Wells NHS Trust resigned on Friday after four years in the post.
Alan Johnson described the deaths of 90 hospital patients from Clostridium difficile as "scandalous".
Kent police have launched an investigation into whether the trust should be prosecuted for the deaths.
The suspension of Ms Gibb's pay is pending legal advice.
Ms Gibb left the trust by mutual arrangement.
The trust said performance had improved under Rose Gibb
The trust has refused to disclose how much money she received after leaving.
Annual accounts showed she earned about £150,000 in salary, £5,000 in benefits and £12,500 in pension in 2006/07.
Geoff Martin of campaign group Health Emergency said: "A severance payment should never have been considered in the first place.
"We have a right to know how much taxpayers' money is involved."
The Healthcare Commission said a "litany" of errors in infection control had caused the "avoidable tragedy".
The commission's report said nurses at the trust were too rushed to wash hands and left patients to lie in their own excrement.
The trust said it had not been prepared for "an outbreak of that size and complexity" but had learned lessons.
Maidstone and Tunbridge Wells Trust's Medical director Dr Malcolm Stewart said managers of trusts were "trying to juggle with many balls".
His own trust was changing the way it offered services internally and externally, opening an independent sector treatment centre, managing a financial deficit as well as applying for foundation trust status.
Mr Johnson said he was shocked by the findings, but denied accusations the problems were caused by staff being put under pressures to meet government A&E targets.
He said copies of the report would now be sent to all trusts so lessons could be learnt.
A Kent Police spokesman said the force was "in the process of reviewing the contents" of the report.
"The purpose of the review is to see if any criminal acts have taken place," he said.
The commission began its investigations amid a string of complaints about cleanliness, and was particularly alarmed after the trust claimed no-one had died from the condition despite admitting there had been hundreds of cases.
It said that seemed highly improbable given that the average death rate is between 6% and 7%.
The watchdog examined a sample of 50 patients out of a total of 345 to whom various causes of death had been attributed, but who were also known to have had C.difficile, between April 2004 and September 2006.
It concluded that C.difficile - a bacterial infection of the gut which mainly affects the elderly - was definitely or probably the main cause of death for 90 patients.
It was definitely a contributing factor in the deaths of a further 124, and a probable factor in another 55.
The Healthcare Commission said that despite Ms Gibbs's resignation, nothing short of a full review of the trust's leadership would be appropriate in the circumstances.
Commodes were not properly cleaned after use
It described the trust as one which had been facing some "serious challenges", not least those brought on by a recent merger.
But it suggested that the board's fixation with meeting financial targets got in the way of making sure safety was a priority, and it accused members of not addressing problems consistently raised by patients and staff.
These included the shortage of nurses, which in turn led to poor care for patients.
Patients with C.difficile were also moved between wards, increasing the risk of infection.
In some instances this was due to concerns about meeting the government's targets for waiting times for treatment in A&E wards, the report said.
Isolation wards were few and far between, and sometimes the infected were simply kept in the middle of the ward.
The commission noted there were "worrying similarities" with the last serious C.difficile outbreak it had investigated at Stoke Mandeville hospital, in which 30 patients died.
MAIDSTONE AND TUNBRIDGE WELLS TRUST
Kent and Sussex Hospital
Both involved old hospitals, both had recently undergone mergers, and at both the boards were "preoccupied with finance".
The commission is urging trusts to treat C.difficile as a condition in its own right, rather than a complicating factor.
In addition, antibiotics should be used with utmost care in treating the condition, as they can easily make it worse by killing the so-called "friendly" bacteria in the gut which help the body fight it.
The government has pledged £140m to tackle C.difficile as part of the Comprehensive Spending Review.