UPDATE:

I've done some more testing and concluded on a couple of things. This will be lenghty. Hopefully, this is useful for anyone who comes back to this post:

I tried a new method of testing where I used the Skip Intro mod in order to cut straight to the temple entrance. From there, I immediatley use the command Setstage MQ07b 80 to trigger the stage of the quest Dues Ex Machina where Karek sets off the boobytrap and incapacitates you, starting the animation where Calia massacres him. This of course saved a lot of time during the process of turning on mods by batches to test if they break the cutscene.

But something interesting happened. First, I noticed that Nemesis does work in addition to the Behavior Pack from Nexus (my apologies to those who worked on it, I'm just frustrated). From there, I started turning mods on, focusing on animation mods (I was highly suspicious of Ultimate Combat and CGO). But to my surprise, I came to a point, where I was basically back at my original mod list, and yet the animation still played out properly.

This bugged me out of course, so I started testing ways of triggering the event. I brought in old saves from my current playthrough thinking that perhaps something was corrupted in my file (this was not the case), and I found out a couple of things...

Using the Setstage MQ07b 80 console command OUTSIDE OF THE INTERIOR CELL (Old Dolthulgrad, Depths) where Karek is located always triggered the animation properly. If you attempt to use this command directly in front of the gate before his boobytrap, the animation WILL be broken. Similarly, attempting to use the command from a distance, but in the same cell, will again result in a broken animation. The only instance where you can walk up to the gate as intended AND trigger the animation is by disabling Nemesis.

So disappointingly, no immediate solution, but this does clear up things. Nemesis and the Behavior pack work perfectly fine. The animations are there and they work, it looks like that the way the scene is triggered is faulty.

I hope this information is useful to anyone willing to fix it, it's very much out of my knowledge base. I know this seems like an exceedingly lengthy post, but it's one of those things that just pulls me out of the immersion, which is a priority for me and I'm sure others.