First off, some facts: Limebloods were lowbloods, ranking between golds and olives. Lows are stated to make up the bulk of the population, which means there were a LOT more limes then there were highbloods. If we assume the number drops significantly between castes, then limes would have the 4th largest overall population, and would most likely outnumber all indigos and higher trolls. Maybe even cerulean/blues and higher.

Each caste going down is treated worse and worse, with each higher caste being trained to take out their anger on those lower than them. So, limes would be the 4th worst treated group in the population.

Next, we have the way troll powers are shown to work- if you're a highblood, they get you better army positions. If you're a lowblood, its a gamble whether you can become and exception like the summoner, or are used as a resource for the empire- like the psiionic/helmsman. The summoners case os stated to be VERY rare. He possessed an incredibly rare psychic ability (animal communion) AND a basically unheard of physical mutation that actually gave him an advantage- his wings. Meanwhile, those possessing goldblood psiionics (which are a combo of telekinesis and energy projection) are turned into living batteries- provided they don't burn out on their own first

If you take Hiveswap as evidence, then we see some trolls (Fokkyl) completely burn through their own energy and get the condition of "necrorot" which forces them to constantly drain energy off others just to live. Rust paiionics seem a bit better, its mostly just telekinesis at a lower level. But high levels come with the SIGNIFICANT drawback of being tormented by the dead (its unclear is this happens to golds as well, or is sollux was just special). Looking at the job prospects of Xefros, the only other rust show to have psiionics; he seems to be stuck wither being a regular rust servant, or going into a dangerous bloodsport that would require him to use his powers constantly to survive. He also showcases that overusing his powers causing huge headaches and feelings of exhaustion- something that fit in line with struggles aradia, sollux, and all the other golds and rusts w/ psiionics we see deal with.

However, we also see that Xefros can use his powersat a much higher level, and with no drawbacks when defending Joey during the game. This implied that while there is a limit to how far one can stretch their abilities (ie. Sollux and the psiionic/helmsman killing themselves), emotions can make them far more powerful

So, where does that leave the limebloods?

Calliope implies that every limeblood had some degree of pyrokinesis (which is backed up by the imposter still being seen as a limeblood after basically failing the pyrokinesis tests- almost like failing just meant you were super weak instead of having no powers), and that that form of psiionic did NOT come with the drawbacks that the golds and rusts delt with

If thats true, then that would be the 4th largest, AND 4th most disenfranchised group of trolls ALL had the ability to create fire, and didn't suffer physical/mental exhustion from using it. That alone would be enough of a ticking time bomb for the leaders to say "fuck it" and kill them all. But I think there are 3 more aspects to that motivation then just this basic numbers risk assessment

Firstly, when it comes to human "peasant" armies, they typically win thanks to sheer numbers ("they can't stop all of us!", anyone?). However, for trolls I don't think that would work. In homestuck proper, Gamzee is shown to be near-unkillable, only losing to being bisected by Kanaya. This sane fate hit Eridan, who's a caste higher then him. Feferi abd Equias were killed by Eridan and Ganzee respectively, and while I don't wanna get side tracked by the nuances of that, its safe to say they'd be fairly hard to kill by normal means as well

In hiveswap, its show repeatedly that indigos are basically impossible for a human to kill, purples are considered that difficult to kill by troll standards, abd that violets can only be killed by regular troll by "stabbing straight through their hearts at a very specific angle with a knife coated in special poison" (paraphrased). With fuchsia being assumedly EVEN WORSE

What's interesting though. Is that we NEVER see trolls go up against fire

Seadwellers are pressure resustant, basically invulnerable, and have shit loads of blood, yes. But like, the sea is cold as balls, so, couldn't we just... Set them on fire???

Much like one of my favorite vampire posts like to being up- most things are pretty fucking weak to being set on fire

Add in the fact that robots also doing really badly in fire, and theres a non-zero chance the pyrokinesis SPECIFICALLY was a huge ass weakness for the empire. I mean, in pesterquest we see that chucking a goddamn mall at eridan doesn't fucking kill him, but we never see that mer-troll on fire. And its not like rusts, bronzes, and golds (or even the midbloods), could just. Get their hands on a shit ton of explosives or flamethrowers. Having easy access to fire could be an advantage we're all grossly underestimating!

Maybe the sheer numbers alone could but stopped, but not if every one of those "peasants" had biological flamethrowers, y'know?

(also it would tie into the sun being a huge problem. Like thematically fire being trolls "weakness" fits in with them burning in their sun. Their sun us freakishly hot/bright. But like, thematically you guys-)

Secondly, even if limes WEREN'T a huge threat on their own, they might have posed some kind of cultural threat

Limes and mutants have a lot of narrative linking- caliborn and calliope, the signless and genocide being linked, the imposter and knakri wearing the differentt colored sweaters, etc.

We know that the signless wasn't a physical threat to the empire, but his ideas were enough of a SOCIAL threat that he was killed, and attempted to be erased from history

Just like the limebloods were

MAYBE the limes just were really cool about having solidarity within themselves. Or treated the lowers castes well. Or refused to serve the higher castes. Maybe they just had to die for inspiring widespread social change. Its not that crazy

Thirdly, there is some evidence of a possible caste upheaval

If you except that all limes had some level of pyrokinesis, then its possible that they consistently made better soldiers/engineers/etc than those higher caste then them. Its one thing for equias to be freakishly strong- possibly more strong then the 3 higher up than him. Or for the summoner ALONE to ruse through the ranks. But if a shit ton of lowbloods were consistantly outperforming olives, jades, teals, and possibly even highbloods. Then they'd call into question their place in the hierarchy. And that would be the worst for the poor tyrannical government

Annnnd as a final ado to all this crap: maybe there wasn't a reason

No, no- hear me out!

Trolls die for the crime of being mildly annoying, or just existing ALL THE TIME

In hiveswap heiress Trizza canonically firebombs lowblood neighborhoods regularly for the lols and/or for fucking selfie lighting

The empress might have had them killed for ANY REASON!

Maybe one was late bringing her food, or she thought they were ugly, or she just wanted to see if she could

Maybe the genocide was just what genocide always is- fucking pointless. And the ideas that these lower-class citizens with little to no rights were "dangerous" to the government was just an excuse to hurt them. LIKE IT ALWAYS IS

...