Should be easy enough to work around this - the fruit-and-veg section would be a (mostly) brand-free zone; camera angles at the tills could exclude sight of branded products; if a scene requires one of the characters to be actively handling a product, but not actually using it as a key element of the plot, a polite letter to a local producer should be sufficient to get the necessary clearance; if all else fails, a shallow depth of field would make most brands on the shelves invisible.
Do you mean the "after hours" lights? Most of the supermarkets I visit at night are as bright as day (other than on their "autism" days)!
From a production point of view, does it have to be a night-time scenario? I've watched many movies featuring a daytime supermarket scene that was filmed in the middle of the night. Admittedly, though, having the story take place outside of normal shopping hours would give it an interesting angle. If you were to set it in the early hours of the morning in a 24-hour store, you'd have a tight, well-balanced group of characters - a few lonely shoppers (why are they buying beans or bananas at 3am?), the guy/girl on the till, someone re-stocking the shelves, a cleaner ...
An elderly friend of mine, giving me dating advice, suggested I hang out around the tills in the local supermarket.
(Yeah, right ... ) Her logic was that you can tell a lot about a person by what they're buying. If you chose the route of character development instead of action, there's potential for a good metaphor there - two people meet at the entrance, repeatedly cross paths at certain symbolic products, their relationship develops as they progress through the aisles, until the finally check out and ...