Assuming #2 is true (there still is no evidence for it), Allah is still just. That’s because Allah has a system and created us in this world to try us. Allah put desires in us, but we are to resist them and only act upon the desires he made lawful. I’ll provide a few examples here:
1- Isn’t arrogance a sin? Put God put it in us. He’s just because he told us our trial is to resist arrogance.
2- The same applies jealousy.
3- What about sexual desires? Didn’t Allah put them in us? But adultery and fornication and masturbation are all haram. What if someone can’t afford marriage? Can they masturbate or fornicate? No, it’s still haram. This person must be patient and resist desires.
4- Some babies are born with defects and disabilities. It’s a lifelong struggle. Didn’t Allah allow it to happen? He is still just because life is a trial and He will compensate this child for all this suffering.
The same can be said about homosexuality. Assuming it’s natural and there is a gene for it, it’s a test. God tests us with health, wealth, and many other tests, and one of them is homosexual tendencies. Remember, the presence of homosexual desires is not a sin. Acting on them and practicing homosexuality is sinful.