senpai is giving last farewell gift because she can't answer that both her and ishigami want to. senpai is not rejecting the idea going out with ishigami, she rejecting the idea of long distance relationship.
while it is not common, it's strange either to do so. she is not a thot, since she is not cheating, and only giving to someone she hold dear into. she thankful ishigami is liking her that much, she felt guilty that she can't answer ishigami feelings properly. remember, she even asking advice to kaguya, which lead to this whole fiasco. this is her best offer she can give to ishigami. she didn't hold ill feelings toward him, or doing it simply out of her own sanctification.
however, ishigami also just that good guy to the core, can't help himself seeing senpai giving such a sacrifice to him. he feel didn't deserve this. hence why he is sad, but he isn't angry except to himself.