I'm not completely certain what wasn't realistic or logical about them. On Thessia, Kai Leng calls backup that Shepard wasn't expecting, on the Citadel he hit Shepard's vehicle.
The unfortunate truth is that in most games mid-boss victories do require cut-scenes that illustrate that victory or then setting the boss to be invulnerable and pummel the player to the ground, which would probably get as many complaints.
So turn this around, what scenario would you have been happy with Kai Leng getting that victory? And in some detail.
Inquisition did this very well in the "In Your Heart Shall Burn" quest where you lost Haven to an enemy assault. No one complains about that feeling forced or contrived. You just legit got your ass kicked by an overwhelming force, because you were in a relatively indefensible position. You still got to be a hero, you still got small victories during the fight, but the over all battle was a route. Something similar happens when you fall into the fade later in the game. You win, but the victory *costs*, and the cost can be very high indeed. Hell, even ME3 does this well earlier in the game, where you're basically forced off Earth by overwhelming enemy numbers.
There's also the wave battle in Arrival. It's legit one of my favorite fights in ME2, because it never feels cheap, even though there is no way to win. In fact, it makes you feel even more heroic because you can "win" in a sense, by making it through all the waves before the final pulse goes off and knocks you on your ass. That's what they could have done to make the temple sequence better. Have Kei Leng directing the fight, throwing wave after wave of Cerberus troops at you, until finally, he just gets fed up, and has his gunships blow out the pillars.