Is it permissible to give a small portion of the end-of-service gratuity as charity, after intending to give most of it as charity, due to working for two companies simultaneously during the notice period, and is this intention considered a vow?

If you did not utter words that indicate commitment, then no vow was made, and no charity is binding upon you. As for your feeling of discomfort due to working in two places and its effect on money, it is unclear, and judgment about a matter is based on its conception.