The 90s Clone Saga was commercially successful even if it was divisive with the fans. Even then the initial parts of the Clone saga were widely popular hence Marvel extended the story way past what the creative team ever intended and focus on the various mysteries which were seen as popular.
I hope when you're talking about Marvel going bankrupt you're not talking literally. Marvel's filing for bankruptcy in the 90s had nothing to do with selling comics. Like I said the various Spidey comics were selling well at the time and even if they were the Spider-Man line collapsing wouldn't have caused Marvel much financial woes. According to some the company would have been kept afloat by X-Men related sales alone.
The reason Slott was chosen as main writer was that his stories during the rotating OMD era were well recieved by fans. Admittedly part of that in my view was because he actually referenced the OMD changes and people suspected he would reverse OMD.They are also very aware of how unpopular OMD/BMD is, and ( at least when Slott wrote the book) did not care what the audience felt. Now can a story be simply bad, and not ruin a character?
Slott's own run was hugely popular stories like Spider-Island and Superior Spider-Man. During his run on the book it was consistently Marvel's top seller which does not support the idea that fans hated his stories or that fans hate his stories or felt that the character had been ruined by OMD.
There definitely is a toxicity within the fandom due to OMD with anyone who doesn't subscribe to the mindset that the character is forever ruined or that Slott was some hate figure is dismissed even if evidence would strongly suggest most people don't feel that way. Personally I don't see a huge difference in characterisation and tone with Spencer's run, it seems very Slott-esque to me save for him being in a relationship with MJ.
Then again the silver lining for Marvel is that after all this if they want fans to laud praises to anything Spider-Man related regardless of quality then getting him with MJ is the magic bullet.