One thing to consider, this has actually come about DUE to the partnership with Etihad (hence the via Abu Dhabi out if all places).
It could work in 2 ways.
Joint venture means that it makes no difference to Jet or Etihad who the passenger uses to get to AUH (or indeed India). Its like the BA/AA/IB venture, all carriers get the same share of profit regardless of who carried them.
Therefore, if Jet ran DEL-AUH-MAN, both carriers get shared profit, Jet gets a visible presence at MAN and Etihad can use Jet as the 3rd, or hopefully by then, 4th daily flight into MAN without tying up their own aircraft.
Also, the 2nd point, AUH would be a scissor hub for Jet, so while the jet airways aircraft may fly MAN-AUH-DEL, the passengers have many options to travel to BOM etc, or use EY to get to MAN if the connections warrant.