Agreed, I'm fine with what was done in the episode. I always thought the light show was not what the person would see when they looked at the Medusan, but a representation of the chaos that sight could bring to their mind.
There were other things about Kolos and his container that I thought were not sufficiently explained, like why the corridors had to be cleared and why the precautions in the transporter room, but overall I like the episode and never had a problem with the light show.
Yes - and it got ridiculous right at the start when Spock took the Visor off as soon as Miranda beaming up with the 'Kolos in a Box'. Then again at the end where they Spock again isn't weaing the Viso UNTIL he goes back to the Transporter Console to beam them to the Medusan ship (yes, I realize the production reason was so they could reuse the first 'beam up' process shot) <--- But story wise that aspect was just a disjointed mess.