Well first off, this is something that does happen on the GMAT. We've all been taught that "have been" and other forms of "to be" contribute to a wordy/awkward sentence structure, BUT when you are given 5 choices, never think about what would have been MORE correct, simply choose the best choice. Introducing a sixth choice may seem like you are thinking of how you could have corrected the sentence even better, but in fact this is dangerous on the GMAT as it prevents you from focusing on the issue of simply choosing the best choice. So put on your GMAT blinders and stick to the 5

A. Misplaced modifier - this changes the meaning by suggesting that the paychecks were assigned to the UN.
B. This correctly modifies the employees, and perfect tense is actually appropriate. The rest of the sentence talks of the present, but the "assigning" happened before, so present perfect correctly conveys this.
C. Having been is a big no no if you have a better choice. Make sure you eliminate all other choices before you ever pick a sentence containing "having been".
D. in place of, is rather unidiomatic. And the "them" is ambiguous.
E. to have been assigned by them, this is grammatically incorrect and changes the meaning.
B is the best choice.
As for your sixth, this could be correct too, since it could mean something general. But remember this path of finding a sixth choice can be dangerous. Good luck!