P = Java APIs are copyrightable
Q = Google has violated Oracle's copyright on Java APIs
Does P imply Q?
In order to answer this question, you must first assume P to be true and then determine whether Q follows consequently.
This is purely a logical/philosophical exercise (that could nonetheless have serious consequences for the outcome of the case); the Judge had to give this instruction. If he told the Jury to assume the opposite, there would be nothing for them to determine (we already know that not P implies not Q).
Indeed, but that was not the question at hand: "when a judge tells the jury to assume something, is he implying there is a good chance that that is how he would judge the case?"
>>> I guess by your reasoning, then yes, he is implying that, otherwise the implication is always true and there's no logic to assuming a false P.
There are two separate questions being asked here:
1. Is P true?
2. If P is true, does Q follow?
The jury is assessing question (2) while the judge will later assess question (1). Question (2) is a question of guilt (if this were the law, did Google violate it?) and question (1) is a question of law (is this actually the law?).
To answer (2), the jury must assume P then evaluate the consequence on Q; that is simply the manner of establishing the validity of a material implication. As you note, if the jury did not assume P, then they would have nothing to do. However, that the judge instructed the jury as such does not indicate any bias on his part; he was simply providing instructions to simplify the procedure of logical reasoning to a group of 12 laypeople. I'm assuming that most of them aren't trained mathematicians, logicians, lawyers, or philosophers.
To put it succintly: the answer to your original question is "No."
Trial is trying to evaluate "P and Q". Judge does not want to evaluate "P" (lazy evaluation?), so he rewrote expression to "Q and P" hoping to short-circuit.
This is purely a logical/philosophical exercise (that could nonetheless have serious consequences for the outcome of the case); the Judge had to give this instruction. If he told the Jury to assume the opposite, there would be nothing for them to determine (we already know that not P implies not Q).