Dear Srivatsav,
You have not mentioned what transpired between the management and yourself in the negotiation based on which you joined the organization or whether the offer was modified officially as a result of such negotiation. Thus, your decision to abscond was prompted by two reasons - one is that you were not served with the appointment orders even after two months of your joining and the other is that you were not given the benefits as promised.
When the employer fails to implement certain clauses as renegotiated even after a lapse of reasonable time, you could have unilaterally terminated the contract of employment by simply resigning. Therefore, it is not clear to me why you chose to abscond instead of resigning and maintained your contact with the manager. Perhaps, you might have an inherent liking for the job or the organization but for the non-issuance of the appointment orders and the non-implementation of certain benefits you desired and the management agreed in the later negotiation. So, can I presume that you staged an abscondence drama just to bring the management to terms?
Legally speaking, you became the employee of the organization even in the absence of an appointment order and served for about two months. Had you felt that the non-compliance of appointment orders and benefits issues are a violation of the employment contract by the employer, you could have submitted your immediate resignation even without notice as an indication of your protest. Else, you could have resigned complying with the notice condition.
Now, by absconding as you admitted, you have subjected yourself to disciplinary proceedings for the misconduct of abandonment of services which may even end in your dismissal and to avert this, the employer can insist on serving the notice period or payment in lieu of notice.
If you are particular about the future of your career as a paid employee, decide accordingly.