Yes, this is the "let's explore racism" episode. And the "let's hit you over the head with racism" angle not withstanding, it makes some other good points on the nature of revolution (as noted, Bele seems to have survived his followers quite neatly) and authority (Lokai having a nasty fascist/political streak).
Performance-wise, Lou Antonio is the better of the two guest stars, both preaching to the crew his litany of hatred, and playing the hot-headed rebel who is also a political self-serving manipulator. Gorshin, unfortunately, comes across as the Riddler. His performance is almost mime-like at times (especially near the end), and other times he's the sneering megalomaniac villain. Still, he gives a good performance as someone who thinks he's from a superior race forced to consort with these "lesser" humans and a Vulcan.
The costume design does them no favors, though, especially Antonio in his skintight white tights and codpiece. Ugh.
The main problem is that the Enterprise crew is pretty much passive through all of this. Shatner gets some overly dramatic speeches, and Nimoy seems more emotionless then ever. DeForest Kelley seems to get out while the getting is good: maybe they thought his presence as a Southerner might strike a little too close to home about racism?
Also maybe it's the fact that even without their hatred, Bele and Lokai are pretty unsympathetic figures. Even before they were torn by the absurdly large 50,000 years of hatred (does such a huge number add anything to the episode?), they were pretty unlikeable jerks. Maybe if they were a law officer and an escaped slave wanted for murder who were gradually twisted into hatred, over a couple of 100 years, rather than a major political officer and the head of the revolutionary underground, they might come across more sympathetic.
As is often the case in the third season, they seem to spend a lot of time saving planets from disaster (see also The Cloud-Minders) and the 2008 remastery teams wastes an opportunity to show the Enterprise actually... doing something above Ariannus. The upgrade of Cheron's surface is nice, though.
Jud Taylor's direction is... odd, to say the least. As has been noted elsewhere, he seems to have been inspired by Gorshin's presence to do 60s Batman-style flourishes like tilted camera angles and zoom ins and outs on Red Alert signals. He never did a Batman episode, though, but his style here is unique compared to his other third-season Trek episodes. He also makes pointless self-destruct sequence suitably suspenseful. (And he remains gainfully employed at least through 2004.)
It's not that the racism angle is that heavy-handed for 60s allegory: in fact, as noted the Enterprise series reused the basic plot decades later. It just has a few too many contrivances. The crew here know all about the legendary semi-mythical Cheron, the two visitors have whatever convenient powers they need, Kirk lets them wander all over the ship, and then they just get off the ship and go ahead and kill each other. It might be some weird argument for the Prime Directive ("They want to kill each other, fine!"), but it still seems odd to just let two advanced beings leave the ship and hunt each other through the ruins (as chilling an image as that might be).
So B for effort, F for subtlety.