The BTS for that story is that Marvel wanted to kill Gambit permanently (or as permanently as possible for Marvel). So far, they were selling the "mysterious" aspect of him not much for what they planned to do with him, but because they didn't have a real background for him. It's the 99 run that finally gives him a good origin. Before that, they were still not sure of where he came from, what was the big secret he was hiding (before that, it was revealed that he got a woman killed for being a moron, I guess they thought it wasn't bad enough), or where his character was heading. So, they just got tired of him.
They later tried to save it saying Rogue absorbed his guilt so she was influenced by him, yadayada, and made them break up amiably. But the character never recovered aside from those two numbers I mentioned above. He just became an accessory of Rogue.
That's actually bullshit.
Gambit was created to be a new identity for Mr Sinister who was going to be revealed to be a mutant immortal stick in a 10 year body because he ages one year every 100 years, that uses avatars to interact with society. And Storm's love interest.
Editorial vetoed the story that would have introduced him/revealed him as Sinister (Mutant War) and Claremont pivoted to Gambit as Wolverine's rival for his "Logan is getting old and can't compete with the new hotshot Xman).
Jim Lee then took over the Xbooks and ditched the Gambit/Storm plan to ship him with Rogue. And set up the idea Gambit had a dark past by having Sabertooth recognize him and be puzzled Gambit was working with the X-Men.
Then Jim Lee left Marvel and Fabian N took over. Fabian wanted Gambit to be a spy for Mr Sinister, granted one who had great reluctance for it. But the character was a huge hit by this point and editor Bob Harras got. BERY protective of Gambit.
The Sabertooth relationship got explained away as Sabertooth killing a former lover when Gambit's cousin pissed off a crime syndicate and Gambit had to pick between his girlfriend and cousin for who would live and Gambit picking blood. But Fabian pushed HARD for the sinister spy at and ultimately quit when he was told he could reveal it but not follow up on it as far asep came frin wanting to keep it a dangling ala Portocio wanting to make Gambit either the Xtraitor or the last surviving X-Men who was sworn to silence over his failure to save the team.
The duck teasing over the reveal about Gambit and Sinister and the Rogue/Gambit/magneto love triangle caused a massive backlash against Gambit in the 90s as it became apparent he was Harras's poochie. Which is where his bad rep came from. Shit came to a head when Scott Lobdell quit the book and Seagle/Kelly were hired. Seagle and Kelly hated Gambit and asked to write him out and run with Rogue/Magneto as a couple. Harras agreed only because he saw this as his chance to finally launch a Gambit ongoing.
Lobdell agreed to write Gambit off ONLY if he got to resolve the Sinister storyline. So we got a massive continuity error filled "reveal" that Gambit organized and formed the Marauders for Sinister and led them into the sewers to killl the Morlocks, which directly contradicted the actual Morlocks Massacre story and how the Marauders found the lair. Gambit is kicked out of the X-Men and plans were made to launch Gambit's ongoing. But fan response to the pay off (and other aspects of the last Lobdell issue) was negative along with fans cheering Gambit's departure that Harras decided to delay Gambit's ongoing until after the 35th anniversary celebration, which saw MASSIVE backlash and generally seen as the was the 90s Golden Age of the franchise.
The hatedom of Gambit was solidified when Harras killed Excalibur to restore the pre mutant massacre X-Men line up for the 35th anniversary and then, to help promote Gambit's ongoing, ordered Scott and Jean cut from the lineup so Gambit could rejoin even though Seagle and Kelly only went through with the editorial ordered revamp on the promise they would still get to be able to do their Dark Phoenix 2 story.
So they refused to follow up the plan Harras forced upon them m to have Gambit possessed by Malice to continue teasing Sinister manipulating him and Fabian N was hired to write the Gambit ongoing, and he hated the Marauders retcon and made Malice be a generic Malice rip off iff and Magneto behind the possession.
The Gambit ongoing only worked if you enjoy Guild of Thieves junk as Fabian write really bad Gambit fanfiction and tried to isolate Gambit best he could from the Xbooks so it has very little crossover with them. Finally there was Wizard pushing Gambit as the third Summers Brother, which got a supreme "fuck no" from fandom
It would take a godly amount of time, until the miligan/Carey X-Men era, for Gambit to be rehabbed and made cool again. But even the , he was exiled from the main books because of how the character spiraled out in the 90s.