1) 니가 여기 없었 으면 좋겠다 = not polite
2) 당신이 여기 없었 으면 좋겠네요 = still not polite, but in the polite form (a suggestion)
Here, the verb "to wish" is not directly translated. I opted to use the turn of phrase, "it would be good if". I guess you can express your wish as the following, but it does not seem natural to me :
내 소원은 네가 여기 없을 거라는거야 (familiar)