The company, as a general rule, has the right to include true and honest facts in a Certificate of Employment in any employment, such as earning capacity and tenure of work. If AWOL was the way an employee ended his employment and that was what really transpired, then they have the right to include such fact there.
Yung option mo na lang nun is to forego having your previous employer as part of your resume when looking for work, since baka mahirapan kang maghanap ng trabaho lalo na kung tatawagan ng mga prospective employers mo yung previous employment mo as to your history there. Alternatively, you may want to amicably talk to the HR department or your supervisor in your previous employment regarding such matter, pero malabo na pagbibigyan ka nila since you did not follow proper procedure in resigning from your work.
In sum, nasa company yung prerogative if they would even give you a Certificate of Employment, and if they will, they have the freedom to put whatever relevant facts they deem important in such certificate.