Agricultural subsidies are ultimately limited by World Trade Organisation rules.
For the European Union the permitted quota is held by the European Commission. When the UK exits the EU it will have no WTO approved subsidy quota in its own right.
Post Brexit the UK will have to negotiate its own WTO agreements. However long that takes in the interim it will have two choices: either cease paying farm support or continue paying illegally and consequently creating a block to the necessary negotiations.
Frankly DEFRA's inefficiencies are going to be the least of the problems facing farmers who rely on CAP payments for significant parts of their incomes.