The club knew that footballing debts had to be repaid in full before any creditors would be dealt with. The FL can make whatever competition rules they like for their competition. Luton Town (same with Leeds) want to play in the competitions so have to agree to them. I can't dictate terms of my car insurance or contract with work to my own liking because I'm benefiting from the services of someone else and have to play with their terms. I can shop around, a possibility not possible in football, but then perhaps Leeds or Luton or even HMRC should challenge the FL's right to insist that football debts are paid off first. I imagine it'd lose in court.
They then still got themselves into a position whereby HMRC could veto the CVA. This meant that, if as rumoured HMRC are the only creditor to have blocked the CVA, their debt was more than 25% of their total debts. Even if you have no intention of running a solvent company you could just keep HMRC paid up (via high interest bank loans if needed) and you'll always be able to escape administration with just the 10 point penalty.
This was an established precedent from Leeds last summer and Luton went into administration mid-November? Even if they'd have fallen into debt everywhere from July-November and paid off HMRC then they'd have been fine.
The question is - what other penalty should there be in this situation?
Clubs that end up in this situation are spending beyond their means and, possibly, signing players that other clubs could've instead (depriving them of affordable playing talent) and taking points off other teams due to players they shouldn't be able to afford and then play. It affects the whole integrity of the league so the punishment must be severe to make it seem very undesirable.