I see it as Marinette showing unconscious biased and being blinded by her friendship with Alya.
In Miraculer the reason she gives to Chat Noir, as to why Chloe can't become Queen Bee again, is because everyone knows Chloe's identity and it is therefore too dangerous as Hawkmoth could use it to trap her and Chat. She says this when it is only her and Chat Noir around, so I believe this is her genuine reason otherwise she could have just said to Chat "I don't trust Chloe because of her past actions." In that episode its not her distrust in Chloe that makes her decide Chloe can never be Queen Bee again, it is her fear that Hawkmoth will use Chloe against them.
When allowing Alya to continue being Rena Rouge, Ladybug probably still has a little voice in head warning her that Hawkmoth knows Alya's identity and that it is dangerous. However, she is more willing to push it aside because Alya is her best friend and would never intentionally betray her. It does show that Ladybug does have her flaws. She wants her best friend to be her support and subconsciously she is also probably thinking how happy having the fox miraculous permanently will make Alya, which in turn will make Marinette happy. Her friendship and trust in Alya is blinding her to the fact that she is unintentionally putting Alya in danger by involving her so much considering Hawkmoth knows Alya is Rena Rouge, whereas because she didn't have a friendship with Chloe she could think more logically about any consequences regarding letting her continue to use the bee miraculous.
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Or it could just be lazy writing and the writers have decided that despite Ladybug knowing the risks and previously acknowledging the risks, they want her forget all those risks and give the fox miraculous permanently to Alya, so that the writers can move the story in a certain direction.