I have not personally crossed the thieves guild, but I knew another agent who did. It made her life annoyingly difficult. The guild’s influence, particularly in The Rift, is very strong.
She could not buy any supplies in the region, those that would sell to her asked absorbent fees, and she was the target of every pickpocket whenever she was inside a city.
I am not particularly eager to live her experience myself if it can be helped.