However, my character Kovin got a very very red lightsaber (6-3 red-yellow) and he's not a darksider so that's a bit confusing. I was going to give him a yellow saber (from my own interpretation). But then I'm still getting the hang of him
As this was created before the morality system, it doesn't include inputs from it. You could always state that in order for someone to have a red lightsaber they must have a morality at or below 20 - otherwise Red is never considered the highest result (in which case it can still shade a saber as the second highest as with Mace).
Personally, I absolutely allow my PCs to develop red lightsabers - because it's one of those moments that makes them react to themselves.
Villains rarely see themselves as villains - and so when a player creates a lightsaber, flips the activator and a ruinous crimson blade springs forth it's one of those shocking moments that makes a character reconsider his motivations (and also makes for awesome roleplay). What usually comes next is the question that ties to Anakin's own fall - you do these things because you believe they are right - but what makes you the decider of right and wrong?