1)
Was he truly a Chacham?
1.
Rashi from Sanhedrin 21a: He was a Chacham to do evil. Ralbag, Abarvenel (6) - he found strategies to do evil. It was harsh in Amnon's eyes to do so (have Bi'ah with her); after Yonadav agreed, he permitted himself to do so.
2.
Malbim: Chacham implies that he uses his Chachmah for the good. This applies also here, like I will explain (refer to 13:5:4:2).