There are several cases where they ignore their political best interest based on values.
I'd rather think the key difference here would be found in a basic element of representative democracy: you can only have an influence during elections, not between them. Ardana was already a member; Bajor was undergoing a selection process. Only the latter situation would allow for the sort of blackmail that makes democracy work.
Spock knew of their existence. The situation with the group called "The Disruptors" seemed to be a surprise
Spock apparently thought of that
situation as a recent development once informed of it, and nothing in the episode indicated otherwise, either.
So perhaps the other situation, the general dissatisfaction of the Troglytes in their lot, is also a recent development? And by extension, perhaps the zenite gas exposure and its related woes are new things, too. Possibly there was less mining previously; possibly the demand for zenite specifically only emerged recently, and old mining procedures that used to be perfectly safe for the Troglytes did not work on the new material at all.
Note that zenite is only found on Ardana and nowhere else - yet the Stratosians keep none of the stuff in stock! It is only mined as a direct response to the crisis on Merak II, apparently. Possibly this is the very first time it has been mined at all (or, to acknowledge the Federation knowledge about the potency of zenite, the second or third time, but the previous times were long, long ago), and the Merak crisis is the root cause of the sudden suffering of the Troglytes.
How sudden, we don't know. The Merak crisis need not have cropped up overnight, and the fight against the plague may have lasted for years already, the zenite mining having been going on for months, and Kirk's courier mission is a carefully scheduled rather than unanticipated one (which is why even the Troglytes are so well informed about it).
Sure, Plasus speaks of "centuries of evolution" having proven that the Trogytes have no potential and deserve no better. But Plasus might be speaking the objective truth there, the Troglytes indeed being a "lower life form" - yet their suffering might still be a very recent thing, a development Plasus' regime is taking joyful advantage of. The preceding High Advisor, a few years back, might not have enjoyed the circumstances yet.
Troglyte life may have been quite idyllic back when Kirk and Spock previously visited this planet... And since the teaser indicates that high warp is called for to reach Ardana, and since Spock has been unable to revisit despite his desire to do so, we could assume outsiders from the Federation heartlands seldom visit Ardana. Hell, outsiders seldom visited Deneva, either - an entire year of complete silence was not considered worth checking up on! Quite possibly, we are only seeing a particularly repulsive Stratosian at the office of High Advisor at a particularly dire moment in Ardanan history, and the two-layer societal structure is otherwise a palatable one by general UFP standards.
How would the Federation handle a cast based system based on biological differences such as the Tholians?
For all we know, Ardana is one. Zenite might simply exaggerate an already existing difference between the two population groups, and this "natural" difference (without zenite influence) might also be but the result of different living conditions, nutrition etc., but that doesn't mean that the biological differences would be any less real - or that the UFP would be obligated to eliminate them by artificial means, such as by forcing every Ardanan on an identical diet.
Just as an aside, the one-city nature of the planet sort of suggests that this is actually a colony (possibly a human one from Earth) that simply has a few centuries of history of isolation behind it, rather than an indigenous society on a planet possessing a full, natural ecosystem. Plasus quoting "centuries of evolution" as opposed to "millions of years" is suggestive as well... But this doesn't mean that every colonist would be obligated to an identical lifestyle or biology.