Jailing him undermines him directly by restricting his freedom. A charge of sexual misconduct will discredit him particular in the mostly-left-at-the-time circles that supported him. Having him in jail in a "friendly" nation also gives you time to prepare your proper, "iron-clad" extradition warrant... because if he is free who knows where he will be once you get your stuff ready.
Note that Assange was in the UK, in full reach of the authorities, for over a year before he claimed asylum in the Ecuadorian embassy. The story you're cooking up simply makes no sense in that context.
PS: the "timeline issue"... asked and answered: https://news.ycombinator.com/item?id=19633178