I play Rao most of the time in season 1. Rao is not a good counter to the stealth helicopter.
1. The range of Raos hacking is very limited, additional, he needs line of sight, it breaks very easy through any obstacle (like trees)
2. The pilot gets the information, that he gets hacked, so he just can pull flares and fly away -> Rao can't do anything against it, the helicopter is too fast or he can break line of sight
3. If you manage to hack the chopper, you have to sent a rocket instantly after this process, if you wait only 0.5 seconds, the flares are up, before the rocket will reach the helicopter
4. After one hit, Rao can just stand there, the helicopter will heal itselt, Rao can do the trick 3x times, then he can't do anything
5. And if that in not enough, the pilot get information on the HUD, where Rao is, so the helicopter just have to use flares, fly away and after the cooldown of flares is ready again, just kill him, as you know where he is.
So everything the helicopter has to do is 2., fly into his base, repeat the attack. Oh, or just kill Rao, as soon as you know, where he is.
The only option is teamwork, but that is a miracle if we are honest. Or other air units, who are fighting the stealth helicopter.
Oh, did I mention, that Rao is completely defenseless, while he is fighting the helicopter, so if he tries to fight the helicopter in the open field, he will just be shoot down by other infantry.