That's a very good question!
I think there's a built-in fannish desire to come up with a story that doesn't involve Blair at all; to say that Ralgha's defection was some larger act of statecraft and that Blair just happened to be there. It's our nature to push against that small universe interpretation and say oh, it must be some larger thing we don't understand…
… but I'll argue that it's actually the opposite case: the Ralgha personality overlay scheme was probably intended as a short term project to target Blair specifically rather than what it became. First let's talk about what's going on with Prince Thrakhath in 2655. Until this point, the war has been run by his father, Lord Gilkarg. With the loss of the Sivar and its fleet, the Emperor has finally had enough: he executes his son and declares Thrakhath the new heir.
Before this, Thrakhath was a very successful fighter pilot and an effective fleet commander whose tactical skills were recognized by the Confederation. While he was not responsible for the loss at Vega or the Sivar debacle, he also wasn't in a flawless position when he was named heir: he'd been roundly defeated at Dolos the previous year, losing his own dreadnought and a significant force of Drakhai in the process. (The loss of the Sivar fleet was particularly egregious because it was a blow specifically to these forces, the ones the Emperor keeps in reserve to consolidate his power).
So what's one of the very first things Thrakhath does when he takes power? The day after the Sivar is destroyed he breaks with the twenty plus year long Kilrathi tradition of not (diplomatically) recognizing the Confederation and issues a public vow that he will be seeking revenge for the death of his father and that he intends to battle Blair in single combat.
From the Kilrathi Saga manual:
<blockquote>
Thrakhath's Vow
In my homeland, the weaker warrior-clan have christened you as the Heart of the Tiger, but to me the human “tiger” must be a beast of small measure. You have not the courage to face a true warrior of Kilrah alone in battle.
I know only hate for you when I hear your name spat from the mouths of my pilots. But rest assured that we will soon meet. My father was Admiral Gilkarg, son of the Emperor. Your death is the price I require for his shame, for it was he who paid for your cowardly attack on Kilrah’s royal fleet. He did not receive a rightful burial, only a dishonorable execution by a lowborn Kilra’hra.
And for that, my enemy, you will suffer greatly. In the eights of moons to come, I too will strip from you something you hold dear.
On my blood and name,
Prince Thrakhath
TRANSLATED BY TCN INTELL: 2655.200
</blockquote>
Again, .200 is THE DAY AFTER the Sivar was destroyed. This all happened very quickly and it's pretty clear that Blair is his specific target. Is he furiously angry at Blair personally? Maybe, or maybe that's statecraft: as he says, the lower clans have recognized Blair's hero status and it may have become something that he needs to deal with.
Consider also the Wing Commander II intro, where the Emperor and Thrakhath specifically discuss "the human pilot who has caused us so much trouble". It's important to them that the Confederation NOT have such a figure. The Emperor is trying to consolidate his power over the clans, a massive reform that he views as much more important than the sideshow of a human war… and he's particularly concerned with movements like the rebellion on Ghorah Khar. So yes they are intentionally sitting around cackling about you and coming up with schemes to end Blair specifically. (I would also argue that this is not paranoia; Kilrathi sociology about such figures is such that they DO eventually end up working Blair into their religion…)
So Thrakhath takes over as heir, issues that vow within a day and Ralgha defects 71 days later. (With Thrakhath specifically traveling to Ghorah Khar to free him after he's fingered by local security!).
What WAS the plan? Almost certainly for all of this to happen much, much sooner. Note that the vow specifies that Blair will suffer "in the eight moons to come". Thrakhath has a plan in mind that's going to take months, not 14 years. So what happened was that as far as Thrakhath and the Emperor was concerned, another one of their counterintelligence projects, Jazz Colson, managed to disgrace Blair and knock him out of the war (the literal thing they're talking about in the intro!). Ralgha wasn't needed and so he was left in place for some future adaptation. What we see in Wing Commander III is picking up an old toy and adapting it for the current situation, not the result of years and years of planning to get to that point.
A couple of other notes:
The Heart of the Tiger name. Thrakhath notes in his vow that it's something that the commoners have already come up with in his 2655 vow, presumably following his celebrity after the Vega Campaign. It's casually mentioned in the Armada manual, too, by the POV Kilrathi who recognizes that the Heart of the Tiger is 'the only human worth fighting Prince Thrakhath one on one'. We also learn in the WC3 novelization that it's called a 'vengeance name' and that while it's very uncommon it's not a case of Blair being the only one to have one; that it signifies a public challenge from a Kilrathi noble (especially unique because Kilrathi rarely recognize humans as their equal). But we also see in the WC3 book that Thrakhath considers "Heart of the Tiger" to refer to the Hobbes option rather than that he's spitting angry about Blair… he treats it as a tool he has to use to deal with Behemoth (and refers to the activation, not the human as "the Heart of the Tiger").
What about killing so many Kilrathi? There's two answers for that, the first is that the Kilrathi aren't especially concerned with death the way humans are. Kilrathi tactics are such that it was not considered a terrible thing that their casualties were three times those of the Confederation. It wasn't until the late 40s that they moved away from trying to overpower the line with suicidal attacks. But the second part is: "... did he?" Both when we meet Hobbes in WC2 and when we see him in WC3 he has contrived some reason to NOT be an active combat pilot. In WC2, he claims Tolwyn doesn't want him doing anything 'important' and then in WC3 he has specifically requested not to be a pilot. It may well be that his overlay is set up in such a way that he tries to avoid combat as much as possible… and instead provides human intelligence with a skewed view of Kilrathi culture/intelligence (noted by Tolwyn later!).
(And then, you mentioned Ariel, we see in the novel that there's actually a pretty complex set of combat rules from Thrakhath for the Kilrathi dealing with Ralgha and Blair specifically… that there are various times where they've specifically been ordered NOT to kill them in combat.)
