Civilization – As Mapuche, does capturing a civilian unit lower enethe loyalty

Loyalty is improved in the following ways (Will add more as I find them),

• Each population provides 1.0 loyalty up to 9 tiles away but are 10% less effective for each tile away.
• Heroic/Golden Ages add 0.5 loyalty per population.
• Dark Ages remove 0.5 loyalty per population.
• Governors established in the city emit +8 loyalty (some can be promoted for more) and other civilizations' governors in nearby cities can reduce your cities' loyalty.
• The happiness level (Amenities) of your city affects loyalty.
• The Limitanei military policy card provides +2 loyalty in a city with a garrisoned unit.
• The city-state Preslav provides +2 loyalty in cities with an Encampment district when Suzerian.
• There are two city projects that can increase loyalty when complete (Break and Circus projects).
• Culture alliances with other civilizations can prevent negative loyalty effects from population of that civilization.
• Recently captured cities (through military) will have loyalty penalties, but these can be ignored with a garrisoned unit inside.
• The Audience Chamber building in the Government Plaza district applies a -2 loyalty penalty to every city without a governor (Thanks to David Harkness).

I found this information in-game on the city panel (loyalty page).

I've tested this a few more times, and from what I can see there is no Warmonger penalty for caputuring a Free City, even if that Free City used to be the last remaining city of an enemy Civilization.

As has been mentioned, this is likely to prevent you suffering a warmonger penalty for taking your own rebellious cities back by force, but it does provide an amusing (if situational) way to wipe out an AI civ without suffering the "captured a Civ's last city" warmonger bonus.