For historical canon accuracy...
(Warning: Long, but interesting reading for those who love CoAS...)
The following are the FOUR distinct endings to the "La Bella Isabella" Quest.
These are the ones that are included on my installation, which was a modified english dialogue and quest version of the original release of the Russian version, and does not take into account GOF or GOF Eras mods.
This is not just text, actual changes in the way this play out in locations.
I think it was removed because it was considered already too complicated.
Personally, I like the "complications" of CoAS quests, because leading players by the hand is amateur with red arrows and "go here" notes.
There are other quests that can end differently as well.
The Flying Dutchman Quest (Ship of Souls) is another one that has a few different endings.
Most people NEVER have seen more than the FIRST Isabella ending, because this coding was removed on the released English version.
To tell you the truth, most people have never seen the first ending either because now the game is over 8 years old....DOH!
Keep in mind all these endings are AFTER marriage meaning the death of Isabella's brother, the escape, the final Salvatore fight, and the assassins in the church.
1) (Most Commonly Known Ending) The player goes to a "bordello" AFTER marriage and gets caught in infidelity and the marriage is annulled after discussion with Rosita.
This can happen at any time after marriage, even before being "locked out" if you do not visit Isabella regularly for dowry and care.
2) (Most Boring) The player does not pay his "dues" for marriage requirements (time period unspecified, but I am pretty sure only at the BEGINNING for a reason, read on) or Isabella runs out of money (god knows how) and the player gets locked out.
The first time is a "warning" with Rosita Hernandez.
The second? time the marriage is annulled.
House is locked and "foreclosed" according to Rosita, and Isabella has returned to Spain because she cannot support herself for living and returned to her family.
3) (Most Interesting) The player visits Isabella after midnight after a minimum of 30 days being gone.
The player discovers a "note" for a secret meeting and Isabella is missing.
Previously after discussions with others in the town and Isabella, it is *hinted* that Isabella is having an affair.
The note states the meeting is being held in the local governor's mansion.
The player enters the mansion goes to the bedroom and discovers the affair between the governor and Isabella.
Isabella initially fails to admit her wrongdoing, and the player challenges the governor to a duel, which is refused, but it replaced by a "second" if the player retorts and refuses to back down.
The duel is held the next day (I do not remember the "hour").
If the duel is won, the governor still turns negative and San Juan becomes PERMANENTLY HOSTILE. (not necessarily Spain however as it is based on overall reputation).
If the player agrees to the refuting the duel, a divorce is conducted and the marriage is annulled (supposedly so the governor get back to being busy in the sheets? who knows).
Getting back to Isabella is a royal pain in the ass if you win the fight, but can only be overcome if the player decides to seize the town and replace the governor (which is what I did).
Isabella does not seem to care either way, which is quite funny based on her opinion UP TO THAT POINT regarding piracy (I think the devs forgot that code with town seizures).
Conditions continue as #1 or #2.
The lock out is permanent, but either way the quest is closed finally.
NOTE:
Seizing San Juan from Spain BEFORE this ending means the affair "terminates" and is never discovered, and basically gets bypassed because you probably either replaced the governor with your own crew permanently, or gave it to your own nation.
There are other game missions and quests that can get screwed up under the same kind of conditions.
4) (Most Evil) The player visits Isabella regularly and pays his "dues".
The player can choose to KILL Isabella, if they are fed up with her whining.
IF the player chooses to KILL their wife, the local guards immediately investigate the house and find Isabella's body. (Similar to what happened with her brother, which makes sense because the Spanish have already been suspicious of the player in the past of his actions).
They attempt to arrest the player.
If the player attacks or resists San Juan turns PERMANENTLY HOSTILE.
This is similar to the escape from Curacao and the governor in the "Killer the Beggars" quest, but there is one final step instead of just "death" by losing a fight.
If the player accepts arrest he is thrown in prison and a short time later, it visited by the governor and he is told that he is sentenced to death (maybe to cover up his infidelity and wrongdoing? who knows) and the "game over" screen occurs with death and the gallows (or whatever death screens are present in the install).
This is why it is a good idea to have backup saves...
A lot of times the developers can be pretty brutal with choices and consequences, but these actually made sense, instead of fighting TEN MAN-O-WARS at one time like in the "Ascold Quest".
"Las maravillas de algunos juegos antiguos..."
Hopefully, a few new players will discover some of the mysteries of POTEHO in the future which flesh out some of the CoAS story background.
It will worth the time to those that know the archaic control scheme...
You should better play this one after you finish all the others or she will observate you too. 
