I would translate "Пусть всё будет так, как ты захочешь" as "May everything turn out as you wish".
Unfortunately, it isn't always possible to make 100% accurate translation.
The particle "пусть" does make sense here. It expresses consent and a wish. A guy agrees with a girl and wants everything to be as she wishes, but he doesn't know for sure if his wish comes true. If we omit "пусть", it will be quite a different sentence: "Всё будет так, как ты захочешь" that means that he is 100% sure that everything will turn out as his girl wishes.
Here are some more examples of its use:
Пусть будет так. Let it be. (a wish and consent)
Хорошо, пусть будет по-твоему. OK, have it your way. (consent)
Пусть они пройдут. Let them through. (permission)
Пусть только попробует, я убью его. Just let him try, I'll kill him (a threat)
Ну и пусть, я всё ещё люблю его. I still love him though. (a concession)
Tell him to get out of here. Пусть убирается отсюда. (an order)