(Note that in all versions, Argon One is no longer invincible. It'll respawn, but it CAN die.)
For "Vanilla" X3TC (or other mods that don't play with Jobs)
No Civilians Basic(Main Link)(Mirror): This mod removes ONLY "Civilian Ship," "Taxi Service," and "Dropship" ships from the game. All the "named civilians" (ie Humanitarian Aid Transporter, Media Service, ect) are left intact. I went to the OCD-liberty of changing a few wares that civilians carry as well, such as all doctor-related ships carrying Invalids. The average person probably will never notice the ware changes unless they have a habit of scanning civilians. I use this version because it leaves the Arena, Casino, and Hospital Ship civilians...which are meat on the table for boarding parties.

No Civilians Full(Main Link)(Mirror): Full-stop No Civilians mod. No civilians of any kind anywhere. This provides the same effect of Graxster's No Civilians Mod but is based on a newer Jobs version to make it v2.5 compatible.
For Ship Rebalance Mod: Continued, Ship Rebalance Mod v0.59 (derelict), or New Ship Rebalance Mod (derelict):
These versions of the mod are based off of Graxster's No Civilians Mod in the above linked thread; most credit here goes to him. I believe I've fixed the random Terran Customs ships floating through Commonwealth space, as well (they were being spawned in 0,0 Kingdom's End instead of the standard -1,-1).
SRM No Civilians Basic(Main Link)(Mirror): Modeled after draffutt's No Civilians for SRM mod, with all of the "named civilians" put back in. Fix for wandering Terran Customs ships.
SRM No Civilians Full(Main Link)(Mirror): Modeled after draffutt's No Civilians for SRM mod. No civilians at all. Fix for wandering Terran Customs ships.
Installation: (pick one method)
Mod method: Extract the .cat and .dat files (named after this mod) into TC's "mods" folder. If this folder does not exist, create it. Be sure to select this mod from TC's splash menu.
Fake Patch method: Extract the .cat and .dat files (named after this mod) into TC's main directory. Rename the files to one above the highest number of your current cat/dat pairs (on a vanilla v2.5 game, this mod will need to be named 10.cat and 10.dat). The mod will work automatically next time the game is run.
This mod is savegame compatible, but expect strange things to happen to civilians for a while in an existing game. Things such as strangely named or unnamed civilians are normal and expected, and should eventually disappear as their current task is completed or they get whacked by bad guys.
There is a Hashes.txt file included in the ZIP that experienced users can use to verify a good download of the mod. This file does not need to be extracted to the game.
Deinstallation:
Simply delete the .cat/.dat files. Your civilians will soon spring back to life and your universe will be good as vanilla. Unless someone else broke your universe, that is.

Coming Soon?
Depending on how OCD I get (or if there's a massive uprising of support for it), I may include a mod that makes every civilian carry wares relevant to their job. It's nothing but a cosmetic change, but hey, why not?

Game Resources Modified/Used:
Jobs.pck edited with X3Editor's Job Editor v1.1.4.1
JobWings.pck edited by hand