Here's a few things...
1) It seems like the main reasons they signed to Sire were that they liked some of the bands on the label and Seymour Stein had courted them. They may well have looked back and felt that they should have asked a few more questions.
2) Sire didn't invest an enormous amount marketing the Smiths. They upped it considerably for Strangeways, but a lot of that money didn't end up getting spent because the band split and so the promotional activity that would have been funded didn't happen. I'm not sure whether this is about Sire being stingy, though. I think it may be more that the Smiths were put in a "college radio" bracket, and so a lot of promotion wasn't seen as the best way to sell records. But Morrissey and Marr may well have felt that the band should have been getting more attention in America and it was down to Sire that they weren't.
3) In Johnny's book, he gives the impression of not really knowing why the Smiths wanted to leave Sire in late 1985. He says that there was suddenly a new lawyer around, who he doesn't give the impression of liking very much, trying to push them in that direction. He says he doesn't know how the lawyer got hired - if he didn't hire him, then we can only presume it was Morrissey, and Morrissey wanted the band to leave Sire for reasons best known to him.
4) It's worth noting that Morrissey re-signed to Sire after the Smiths split.