C.O.
There is a difference between having control over her personal space and safety and cleanliness...
YOU are the mom - YOU are in control - NOT her. Yes, it's HER room, however, she lives under your roof so she has rules to follow and obey.
Explain to her what YOU want her to have in her room...if she can't follow those rules, then YOU will clean it to YOUR standards and if she doesn't like it - she needs to do it herself.
I wouldn't worry about her losing trust in you - you are the mom - not her friend - that will come when she's an adult...you are not throwing her stuff out you are organizing it...
GOOD LUCK!