It's perfectly fine to make changes now.
Few notes:
In the original font, the letters in charset.png are 16x16 pixels, but they are actually 8x8 scaled by 2. This means you should ideally treat a 4x4 block as a single pixel. So, it's best to avoid 3‑pixel‑wide lines and especially 1‑pixel elements, if possible. Ideally, charset.png should be a 2x version of charset_small.png.
This isn't just about visual style: 3 and 1‑pixel elements are more likely to scale poorly in‑game. However, these rules aren't absolute; sometimes you have to break them to make a letter look correct.
In this case, the red‑marked pixels will do more harm than good, unless the letter becomes unreadable without them:
For Φ and Ψ, it's better to remove the red‑marked pixels. However, this isn't mandatory, if keeping them makes the letters look significantly better, it's fine to sacrifice the black outline for readability.
Everything else looks fine - good job!
Ultimately, though, the final look of the letters is up to you - since I can't read Greek, I trust your judgment on what looks best.