No. It actually sucks, because it leaves the red templars as dead, necrotizing plot flesh.
Huh? The red templars show up all over the place. In fact, I would claim that CotJ makes their later appearance more logical. If Therinfal's templars were corrupted, and then wasted at Haven, why would anyone want to join them? On the other hand, if they're stopped at Therinfal, then the world doesn't really learn of their true horror. It's all overshadowed by the Inquisition recruiting the templars. So none of them really know what red lyrium does in that case, and more templars are willing to try it.
While Samson's story isn't amazing, the red templars have no plot or point without him, whereas the Venatori are handled perfectly well through other Inquisitor's Path quests.
They have plot and point. They would still exist as vicious marauders who spread Corypheus' precious red lyrium everywhere they go. They grow the red lyrium, they protect it, they help transport it.
If you think red templars are lacking in plot or point without Samson, then just how do they have purpose with Samson still alive? They still do all the same stuff. Only I guess they do more searching for artifacts and spread more red lyrium with Samson.
Additionally, In Your Heart Shall Burn is far better when fighting the red templars and having them be revealed as Corypheus' army, with the Venatori being revealed earlier as sneaky, subversive types.
Better how? More horrifying? I guess. But CotJ gives us a horror-filled battle against red templars as well. The only real sticking point I saw with the red templars attacking Haven was when Behemoth Denam showed up. That was the only "well, sh!t" moment. However, you don't even meet Denam in that path, so he's just some nobody to you. In the CotJ line, you have already met Fiona, and that is the better "well, sh!t" moment because you actually have met her at least, spoken to her and learned about her in Redcliffe at most. And yet there she is trying to kill you.
It could also be argued that the Venatori are "better" because they are people, still in control of their minds. They fight willingly. The red templars are just mindless monsters.
The Venatori are better adversaries all around. They are better equipped to search for artifacts, plan attacks and infiltration efforts, and command the red templars to defend points of interest. Samson isn't needed for anything.
Killing the Venatori at Haven is also the more painful blow against Corypheus. If you wipe out all those Venatori, then logically his forces will be weaker after that. However, if you wipe out a bunch of red templars, the Venatori army should still exist elsewhere, and logically Calpernia should still be leading them, but she's not.
Champions of the Just has the red templars first appear as mindless mooks who aren't even given focus in their introductory quest (said focus instead falling on the envy demon), with the Venatori appearing outside their specialization as an army.
The Venatori are an army as well since they have soporotti. It could also be argued that from a strategic standpoint, the Herald would rather have an army of normal men as enemies rather than corrupted monsters.
I liked having CotJ split between red templars and Envy. It kept the whole thing fresh and dynamic. IHW just centered around getting back to the present, basically.
We learn more about red lyrium by going for the templars. This is info that is relevant to the rest of the game. If you miss CotJ you miss out on that storyline. What do you miss out on by rejecting IHW?
Also, the Emerald Graves plot is mostly devoted to Freemen backstory and gives nothing to the red templars, and Emprise du Lion is still practically worthless without Samson. Finally, Calpernia and her plot are badly underutilized in this game, and Calpernia will almost certainly be in the next one, so there's no need to pounce on it right now.
The Freemen were nothing more than bandits with different skins. Their story arc was meaningless. Still, their main role was selling slaves to the red templars, so the reds still had the dominant storyline.
I don't see how Emprise du Lion is worthless without Samson. Seemed pretty straightforward. Enslave people to mine red lyrium by the order of Captain Who-gives-a-crap. Anyone can replace Samson as a commander, even Carrol.
But if Calpernia is in the next game, and she probably will be, doesn't it make sense to learn about her now AND be involved in a choice that will likely affect her attitude in the next game (that is the choice to turn her against Corypheus or defeat her in combat)? Samson's just a complete... nuthin'.
What, marching over mountains? Aside from the fact that an army of that size is going to be conspicuous no matter what, that environment is much better suited to the enhanced strength and stamina of the red templars.
From a strategic standpoint, you would want your enemy to have those less suited to the environment. Also keep in mind that losing those red templars at Haven just means Corypheus only lost those he gained at Therinfal, while the Venatori remain strong as ever (just with a few less mages than they would have had).
Calpernia's perspective can't be treated with any kind of adequate depth, though. As such, it winds up being ill-fitting within the story. Additionally, having Samson be mentioned as important and then just never show up at all feels rather worse.
But he's not important in CotJ. He's just "S" which could stand for "sh!t" for all we know, and in reality does. He basically entrusted a demon of ENVY to stick to someone else's plan and not form its own plan, all while he went off somewhere and snorted lyrium dust.
And like I wrote above, Samson being Cory's chosen automatically pushes Calpernia off to the sidelines, in which case she isn't utilized at all. By your own logic, Calpernia should be as utilized as possible, yes? So doing IHW negates her depth completely, while a loser character gets a little more undeserved exposure.
Maybe not, but the red templars will still be better.
Look, even if red templars were more fun to fight, CotJ gives us that opportunity as well, and it takes place in an actual castle, not that jumbled mess Redcliffe Castle was turned into. Even Connor couldn't stand the level design.

At least with In Hushed Whispers, you don't have two characters whose plots are abruptly cut short.
Well, Calpernia's is cut. Ser Barris' is cut. And we never get to meet Lord Abernache, a true crime. Nor can we team him up with Movran in this case.
Well, which army is picked for that quest has nothing to do with any of this. But it's a better introduction for the templars than it is for the Venatori, whose main specialization is being sneaky and subversive.
The Venatori can do it all though. And I think the better intro for the red templars is the place in which they became red templars. Not only do we see how it happened, but we save many templars' lives in the process.