Depends on how it's done, but maybe. If it's an added Pokestop with the companies name and picture, and maybe on certain days they can promote (outside of the game) that certain in-game items will be guaranteed to be given at their Pokestop, or certain Pokemon might show up that day (based on an agreement with Niantic), then I don't see any issues with that.

Like for example I remember when Gamestop offered download codes when people visited their shops to get a specific Pokemon in Pokemon X and Y, for example. That seems fine to me.

But if it gets to the point (as it often does), that company Pokestops are advertised from other Pokestops, or the screen gets completely taken over (think a website where the entire border of the site is an ad for one company) and there's autoplaying videos and they tell you to go to their place for REAL WORLD items (like Burger King says "Try our new Bacon Double Taco Whopper!"), then that will suck and I'll stop playing the game.

I'm already sick of dealing with it on websites, I don't want to deal with that while playing games too.