Sadly, there is no convenient way for me to give you the option to just switch single units off and on. All tries i made in that direction have been met by game crashes or to situations where the game would crash when i update my mod the next time... so here's the less convenient way.

In Better Advent's install folder, you will find a subfolder "Config" with all kinds of ini files. One of them, the "XComGameData_CharacterStats.ini" has the values for all unis added by Better Advent. Among those values is the "Spawnweight", which determines how often the unit appears. By setting the spawnweights to 0, you can disable that unit.

First, find the unit you want to disable in the file.
Then, in its values, look for something similar to this:

+LeaderLevelSpawnWeights=(MinForceLevel=1, MaxForceLevel=6, SpawnWeight=8.5, MaxAlertSpawnWeight=9)
+FollowerLevelSpawnWeights=(MinForceLevel=1, MaxForceLevel=6, SpawnWeight=17, MaxAlertSpawnWeight=9)
+UntetheredLeaderLevelSpawnWeights=(MinForceLevel=1, MaxForceLevel=6, SpawnWeight=17, MaxAlertSpawnWeight=9)

Change all Spawnweights and MaxAlertSpawnWeights to 0 and the unit can't spawn anymore. Take note that units may have different tiers, like Troopers and Captains that have 3 or even 4 tiers. If you'd want to completely disable a unit, you'd need to disable all of its tiers.

A few caveats:

#1: When i update my mod (every 14 days currently), that update will overwrite your changed values and reset them to default.
#2: Missions that are spawned on your hologlobe do already have their pods determined. So your changes will only apply to newly spawned missions.
#3: Theoretically, you could break things here by disabling all followers to a unit or something like that. Use common sense.