Working on a program which helps with the running of a supermarket, which includes sale of alcohol
With regard to alcohol, it is not permissible to drink it, carry it, sell it, buy it or help with it in any way whatsoever, such as documenting it or recording it in a book or on a computer, because of the warning and curse which is mentioned concerning it, as it was narrated by Abu Dawood (3674) and Ibn Maajah (3380) that Ibn ‘Umar (may Allaah be pleased with him) said: The Messenger of Allaah (blessings and peace of Allaah be upon him) said: “May Allaah curse wine, the one who drinks it, the one who pours it, the one who sells it, the one who buys it, the one who squeezes (the grapes etc), the one for whom it is squeezed, the one who carries it and the one to whom it is carried.” Classed as saheeh by al-Albaani in Saheeh Abi Dawood.
If part of your job is to record or process things that have to do with alcohol, it is not permissible for you to do that.
But if you can work and avoid anything that has to do with alcohol so that others can deal with that, there is nothing wrong with it. It is not permissible for them to force you to pay three months salary, because your leaving the job is only because of them; they are the ones who have transgressed the sacred limits of Allaah and disobeyed Him.
If you cannot find any way to disassociate from them and you do not have any money with which to pay this amount, and that would result in great harm such as imprisonment, then you are being forced to do that, and there is no sin on you if you work with them for three months. But if your not paying this money will not result in any major harm, then do not work with them, because in that case you are not being forced.
We ask Allaah to bless you with halaal provision and beneficial work, and to increase you in knowledge and guidance.
And Allaah knows best.