okay... so it is indeed impossible to acquire the trophy "Liberty City (5)" after killing Dwayne.
No, you have Roman, Brucie, Little Jacob, Packie. You just need those four above 90%.
Once they are above the 90% the game counts it as done, so you could have Brucie at 90% and the others at 85%. Then if Brucie falls below 90% it's ok, because the game counts the 90% as 'completed' so then just focus on the others.
It's tedious to do the achievement but it's possible to take the friend out on every possible thing on their phone list in one go. So you could say, take Little Jacob out drinking, so do everything else first - darts, pool, strip club, eating then finally go drinking. This makes getting their % up faster.
the number 5 in the trophy title indicates that you must have 5 friends at the required level. i killed dwayne, and had 3 out 4 of the other friends at 100%. after getting packie to 94%, there was no sign of a trophy. (note that the trophies seem to take around 10seconds to actually be rewarded, they are awarded after the auto-save. but i waited for like a whole minute. also note that their level has to be, as stated in the trophy description, ABOVE 90%.) after going back before that point on a different save to kill playboy x, i was then able to achieve the trophy.
i also spent like 3 hours trying to obtain exactly 90% on one of them. in the end i was able to do this, and still didn't receive any trophy. it was possible to use this test with having at least 2 friends that didn't meet the requirements. after getting packie to exactly 90%, i raised dwayne above 90%. again, no trophy... all 5 friends were 90%, or higher. HOWEVER, after taking packie up to 96% with a game of darts i was able to obtain the trophy.
anyhow, since you can't obtain 5 friends without dwayne... killing him makes it impossible to obtain the trophy. but as for the thing you said about them only having to reach a certain level once, i don't know... never thought to test that.
killing Dwayne makes it impossible to obtain the "Liberty City (5)" trophy on the PS3. without Dwayne, you have only 4 friends left.