Honshu:
Not in my experience. "Good" is a game mechanic, nothing more. Essentially, the game asks you to choose from 3 differently valued choices with repercussions down the line. Choosing "Good" simply means that you can opt to align with Good with no costs. Do this experiment and you'll see: rename the alignments and remove all nongame elements.
The "weirdness" of the choice balance will become apparent. Of course, if you're up for score, you need to play a certain way, and that way skews to the Evil alignment, but then again, if you want to max score in other games, you also kind of need to play in unorthodox manners as well.
What benefits does aligning with Good do? It essentially allows you an "in" into a Good-only members club, something that only usually applies to Good Civs. Evil Civs don't usually band up and dogpile people like that. Good Civs do. Is that an unusual situation? Well, you can make your own Civ makeup for the game, so it's only as unusual as you want it to be.
Generally, half component of Good Civs in a game, or equal component of them, all things being equal, leads to a slight domination by Good Civs because they dogpile. The Altarian's superability only encourages the tendency even more. That means that Evil AIs and players need brute power to compete or they'll get dogpiled one at a time.
Yes' I've seen it happen occasionally. Good Civs that are technically individually weak eventually take over a game because they dogpile Evil Civs.
Aligning with Good gives you diplomacy and loyalty bonuses, as well as a substantial Trade bonus. Including the dogpile bonus, it's a little more flexible for peace and war than Neutral (more peace) or Evil (more war), but as an alignment, Good is overall better for winning games (not necessarily for making scores).
The extra wartime techs are a no-brainer. Evil Civs have ship production bonuses and the Psyonic Beam, but if you're not into beams, you won't get that synergy. Good Civs get powerful Armor and Shield techs, and with the premium the game rewards in the midgame for defense-oriented ship design, it's usually enough to score a definite edge in war, all other things aside from alignment being equal.
The attack values and ship fleets I've been able to amass as Evil Krynn, for instance are enormous, especially driven by the bonuses I get early game, but I tend to dominate space combat more as Good anything, because the defense techs are just that uber.
In peacetime, too, the loyalty and diplomacy benefits are palpable. You get more Econ with Evil, plus the free combat upgrades on the starbases, but the trade bonus can potentially make it up, and the tech trade premiums with the diplomacy bonus is also pretty decent.
The MCC is quite potent - there's no doubt about that. At the same time, I do kind of get more surrenders, even from Evil Civs, when I parlay the "surrender to me" aspect of the Good alignment. Getting an entire Civ with such minimal effort is just game-swinging.
The choices on the events are weirdly balanced, not completely imbalanced. You can be Good in the game even if you commit genocide or do slavery. Don't pay attention to that. If you're talking game balance, then we're talking game mechanics exclusively. Whether you choose one choice more is immaterial. As long as you skew enough to Good or Evil or Neutral is the ONLY thing that matters.
What you want is not to balance the alignments, but to balance the choices at the event level. That's not the same thing. Protoss units don't need to individually be equal to Terran units because there are downsides to them elsewhere.
Good choices don't need to be balanced with Evil choices at the event level because there are upsides to it elsewhere.
