Neither Morrissey not Alain has ever made an official statement, but from the bits of info people have managed to prise out it certainly appears that Alain was pushed out of the band by Moz, initially for health reasons, and was very upset when he had to leave. He was in tears on stage at his last gig in Dublin, and despite Morrissey assuring people his absense was temporary and he wasn't being replaced by Jesse, when it came time to record Years of Refusal he was refused entry to the recording studio and effectively given the boot. He'd already been axed away from the live band, now he wasn't wanted in the studio, and since then his songwriting partnership with Morrissey ended. I guess Moz just prefered Jesse and thought it was time to make a clean break, which was one of the most stupid things he's ever done.
Alain could just spend the rest of his life sitting by his guitar, crying, and waiting for Morrissey to change his mind...but instead he's happily getting on and making a succesful music career with other people. Not sure why people are bitching about that. What the hell do they expect him to do?
Pure speculation this bit - but 'I'm OK by myself'. A lot of people thought that might be a lyrical reference to Johnny Marr, but really - it's been so many years I'm sure Moz is well over that particular bust up. I wonder if the song was actually about Alain?