The name’s meaning will not change based on English spellings as long as it’s pronounced properly. My son is almost 8 years old and we named him Eesa and we find that almost 95% of the time it is pronounced properly with Eesa (Ee-sa). He has a class fellow also named Eesa but spelled Isa and his name is mispronounced all the time. Mostly everyone says I-sa (like the letter I +sa).
I suggest naming your son with the spelling Eesa.