If you see improvement in him, then don't stop. Just be careful with the MelaFix. I'm not saying to not use it under any circumstances.
I used it with my betta in a one gallon bowl. He was very stressed, lethargic, and once, after a dose, he fell like a rock to the bottom of the bowl. I immediately did a complete water change, and he perked up.
MelaFix can affect the betta's labyrinth organ (the organ that they use to pull oxygen from the air). It would be somewhat similar to us breathing in a noxious gas. So watch your betta carefully for signs of stress, and be prepared to do a large water change. I was just thinking that your betta already had been stressed, and this may further stress him.
Some members here have had success with their bettas in MelaFix, but their bettas were in larger (15 gallon, I think) tanks.
So, continue to use it, but just be watchful. What dose are you using? I used 1/8 of a teaspoon in my gallon bowl. Also, I wouldn't use it for more than 3 more days. Good luck, and I hope the betta continues to improve!