I'm a little more skeptical here on the audio not being discovered for two years.
They already had a moment during interview #1 where a hot-mic came into play, and that was hugely important moment in the series. When he comes out of the bathroom after interview #2, someone has to take the mic off of him (or at least get it back from him in some way) -- that more often then not has to set off a red flag.
I think the possible motives for Jarecki keeping the audio a secret for are easy to understand. No matter what moral obligation he may feel, as a filmmaker, his #1 goal here is to delivery a compelling product.
Assuming a scenario where he did find the audio shortly after interview #2...If he turns it over to authorities right away (along with the letter) there is a good chance they arrest Durst in the months following. In my opinion, that blows the wad, and substantially takes away from the impact of the film (which is 2+ years away from seeing the light of day at that point).
Put yourself in Jarecki's shoes (again, if you found the audio immediately):
Turn over the audio along with the letter and potentially sacrifice the impact of what you know is a guaranteed historic piece of filmmaking (his life's work)
Give the authorities only the letter to work off of (a big deal in itself), proceed with working on documentary, and then pretend to discover the audio six months before the air-date when the project is just about wrapped
If you give everything to the authorities 2+ years before your air date, arrests and public info will certainly come out before the show sees the light of day. There goes the element of surprise, which is the very thing that made the finale, and in turn, the series, so incredible.
On the moral question, think of it like this. Jarecki's 4+ years of working on the doc led to more justice and answers than authorities accomplished in 40 years. Would you feel like you were owed the ability to show the audio and close the case on your terms?