"PR agency" is quite the stretch. If you read the actual email (
https://wikileaks.org/dnc-emails/emailid/10634) instead of the poor secondhand accounts you linked, you'll see that there's a staffer that says "I think it’s as good as we could hope for. We were able to keep him from including more on the JVF"
This is a staffer saying that they talked the reporter from the NYT out of focusing on an area they didn't like. It shows the Hilary campaign is slimey, but it doesn't mean that the NYT has suddenly lost all credibility as a news source. It's not clear from the email that the reporter actually promised anything; it sounds equally probable that the Clinton people were just happy with the NYT's reporting.
I also think (perhaps cynically) that this happens all the time, and is not a huge deal - sources try to angle the pieces journalists write about them, and selectively reveal information favorable to them, and journalists comply to varying degrees to get more information out of those sources in the future; it's not an ethical bright line - it's murky, and I doubt if you listened to all the communication that journalists had with their sources, you would find some stark ethical boundary between sources and journalists 100% of the time.
All reporters talk to the people they are covering. There is always a risk of sources having undue control over a story, but this doesn't sound as extreme as you are making it out to be. We can't abandon a respected source of journalism just because there is a vague appearance of impropriety.