I think the elephant in the room is the fact that Green may still be injured. He hasn't really had a good defensive game since he went out in that Nuggets game. If he's still hampered, then he ISN'T a good player to defend Ellis, nor does he provide a ton of general help to the team if he's not being left open. I hope that's not the case, because the team is absolutely dead in the water going forward if Green isn't 100 percent.
Provided that that's not the case, Pop is being absurdly stubborn to the extent that this could really hurt the team outside of this series. Danny was too important to the team going down the stretch for Pop to toss him aside at the first sign of adversity, especially while he continues to allow Mills and Beli (and the Big Three to a lesser extent) to work out of their slumps. I think Pop's convinced that Leonard is a superior defender to Green, even though the stats don't bear that out. He seems to consider Danny to be a secondary perimeter defender who only gets an opportunity to guard the opposing team's first option when Leonard isn't in the game. If the Spurs can win this series and advance to face Portland, Pop could absolutely tank the team by putting Leonard on Lillard (against whom Kawhi's never done well) as opposed to Green (who's probably been the most successful player in the league at defending Lillard).
Offensively, I think Pop is valuing folks getting their own shot seeing as the system is breaking down. As far as I see it, he needs to work harder to get the team to generate good looks for Green and everyone else who's struggling by calling more plays instead of just letting things flow. Or he needs to accept that the Big Three (along with Splitter and now Diaw hopefully) are going to carry the team offensively, which means he needs to let Green and Leonard play as much as possible to slow down Dallas on the other end. What he can't do is waffle in between those two and play glass cannons like Beli significant minutes because he's hoping they can pull more points out of their asses without having plays called for them than they give up on the other end.