What I understand from your query is that the salary is bifurcated into certain allowances in your establishment and someone is not interested for the deductions of EPF and you want to fix his all inclusive wages / salary as Basic wage to avoid EPF.
First of all, if an employee insists for non deduction, you should convince him and even if he is still adamant, consider otherwise but it can not be termed as fair. It is definitely termed as unfair practice and moreover, the inspecting authority can raise demand of contribution at any later stage.
So there is nothing to stop you from putting all salary in basic.
However, the same must match with your salary structure
If others have 5 components and this one employee has just basic, it will not be accepted by the department.
Also remember that items like bonus and gratuity is on basic. So you get a cascade im0act on it later