Actually the explanation to why it didn't absorb Susanoo is simple, because it can't. Shinju doesn't posses the Rinnegan ability to reconvert jutsu into chakra and absorb it or anything like that. In reality, the alliance ninja simply didn't try to fight it back, the only one seen fighting back is Madara and he chops through it as if it was a normal wood (bottom right panel):
then we see Tobirama using an actual jutsu that is fuel by chakr and it also cuts through it easily:
then we see Hiruzen simply smash through it:
then we see Sasuke doing exactly the same, but at a bigger scale:
perhaps one should say that Shinju is weak against cut attacks .
Those shown and Bee are seemingly the only ones that tried to fight back and have done it successfully. The fear and mass panic is what caused all those bodies to pill up. It's possible that what Sasuke was disappointed, might have been actually the Shinobi's reaction. That is also the reason why Sasuke jumped forward with a big Susanoo attack, to show everyone that the Tree can be injured, that they can fight it back and they should. Then some Naruto hardship flashbacks, jump up to front and everyone is again motivated to fight.
Both Sasuke and Naruto acted like true leaders. Sasuke by showing the way to defeat it and that it can be defeated (invoking hope), while Naruto by raising the army's morale (invoking will). Looks like the manga might really end by the Senju and Uchiha joining and cooperating for real this time, thus bringing peace, which was one of the possible interpretations of the Tablet that Madara had spoken about.