Is it permissible for me to keep the wages I received during a period of my work in which I was negligent, or must I return a portion of it to the employer, and how should I act if repayment is obligatory, given my extreme reluctance to confront him?

If you fell short in your work and did not perform it as required, then you must return to the employer what exceeds what you deserve, or seek his absolution. It is not enough to leave some of your salary in the company. Rather, the due money must enter the employer's possession, and you should not give him its value in another form. It is not a condition to inform the employer of what happened; it suffices to return his right, even without his knowledge.