Is it permissible for the association to repay a debt incurred by an employee to help Muslim Burmese migrants purchase medicine, using Zakat funds or charity funds?

The amount you took is a debt upon you, not upon the society, unless you were authorized to take the money and disburse it to the poor on behalf of the society. If you were not authorized, then it is not permissible to repay this debt from Zakat (definition) funds, because you are not among its rightful recipients, and this would be considered disbursing Zakat to those who are not entitled to it. The same applies to charity funds designated for the needy by donors; it is not permissible to disburse them except for the purpose specified by the donor.