Is it permissible to take from the company's trust to compensate for a meal allowance that was unjustly deducted, or is it better to leave it to avoid doubts?

If the meal allowance agreed upon with the company is appended to and an integral part of the salary, then the company must fulfill it, and you are permitted to demand it. If you are unable to obtain your right through demand, you may take it from the company's funds under what is known as "obtaining one's right by force" (al-Zafar bi al-Haqq), with conditions including: inability to obtain the right through demand, not taking more than your right, and ensuring that you will not be accused of theft or betrayal. However, it is preferable not to do so for two reasons: First: The issue of "obtaining one's right by force" is a matter of ijtihad (definition) (independent reasoning) and considerable scholarly disagreement. Second: Due to the company's financial problems, showing sympathy and waiving this amount is what good sportsmanship (muru'ah) requires.