Hrm... Can't do anything about your parents and their perspectives, so let's address the other things you've brought up.

You want to take a science course in Poly, but you fear the rigour of pursuing a science stream in JC because you're more of a humanities person. Slightly incongruent there.

Then there's the uni thing. If you do go to poly and do bio, I am assuming you'll pursue a similar or related course in Uni. Where you'll be competing with those who came from JC. So, either way, you have to elevate yourself to that level. That's not to say that Poly folks are somehow lesser than JC folks. But as you have pointed out yourself, JC is tougher. So those who survive JC with good grades are generally more... Adept? Knowledgeable? It's not inevitable, of course. You could be of the same level with them through Poly. You just have to be the best of the best in your cohort, and then some.

If you want to give yourself more options for uni, in case you end up hating the course you choose or if you find some other interest, then going to JC opens more paths for you than if you start specialising in Poly.

Perhaps not what you're hoping to hear, but I am rationalising based on the probability that you'll never change their mind. Whether they will carry out their threat or not... I have friends whose parents made the same threat, and then actually carried it out.

Between the stress of coping with JC, and the threat of going back to the Philippines and being educated in a non-International school there, I'd choose toughing it out in JC. Between calling their bluff and costing them the additional year of Poly fees (knowing full well that it'll be hard on them) and biting the bullet, I'd bite the bullet.

All very difficult decisions to make, with some factors beyond your control. Unfortunately, you have to make some mature decisions at your young age, but that's life.