This is my take on it, fwiw:
He's more interested in the physical sciences than he is in the science classes offered next year. He's not shown the motivation to turn in the boring busy work that makes up homework... even though it seems from what you've written that the policy for grading homework based on completion was clearly stated up front. He's told you that he doesn't care about fighting to be in the honors science class because he'd like to have one "easy" class next year. And... he's 14.
So if he was my ds, I'd not advocate to put him in the honors class. He's told you what he wants to do. At this point, it sounds like it's 100% you wanting him there - if he really wanted to get in, he could have turned in his homework no matter how boring it is or how much he disagrees with the teacher or how insane the teacher is or whatever.
I totally understand how frustrating this is for you - but at 14 I think it's time to start letting our children experience some of the consequences of not towing the line when they need to. I also don't see this as a significant problem looking down the road re college apps etc - if he is really truly passionate about science, and he ends up in a boringly slow biology class in 9th grade, he still most likely can turn that around by doing well in his boring biology class and advocating for himself with the school to put him into honors physics or honors chemistry the following year.
If this was a case where he actually wanted to be in the honors section.. I think my suggestion for this coming year would be to take biology *this* summer and test out of the requirement all together, and advocate to place him in honors physics or honors chemistry as a 9th grader.
My 2 cents - most likely not worth much!
Best wishes,
polarbear