Is it permissible to deal with a website that offers both permissible and impermissible goods, and to donate the value of the impermissible goods?

This action is permissible under two conditions: that you are unaware of the type of goods the customer desires, and that most of the displayed goods are permissible (halal (definition)). However, if you know that the customer wants a prohibited (haram (definition)) item, it is not permissible for you to assist him in purchasing it, even if you intend to give the commission as charity. This is because the intention to give ill-gotten gains as charity does not permit engaging in a forbidden act from the outset. But if it becomes clear to you after the purchase that he acquired a forbidden item, then you must take out the equivalent amount from the commission and give it as charity to the poor.