How did it possibly get to this stage? If you don't have the money upfront then you just agree a "time to pay" deal with HMRC and pay in installments and... that's it. We did that at work during the recession when the money set aside for paying the VAT in one lump sum had basically been raided to pay wages and other expenses and we didn't have the money to pay everything for the year in a lump sum. Hence, broken down into a payment plan and everybody moves on with life.
We haven't had HMRC try to wind us up, at least not in any other way than the business owners yearly exclamation of "HOW F****** MUCH?!" when the yearly tax bill arrives.
One would expect that winding up petitions are somewhat more difficult to arrive at than missing a letter or a single payment.