From my perspective there seems to be alot of grey in the moral issues of this case. The majority of middle-class Indonesian's are happy to overlook his crimes out of respect for the economic stability that they enjoyed during those times. Many Indonesian's claim that they enjoyed more prosperity under Soeharto then they currently do. the same can't be said to families who had their father or brothers mysteriously "disappear".
One blogger asks these questions:
My thought's on this? Well, I'll post an essay soon about my thought on this and similiar situations, but in the meantime let me state - Abuses of human rights (read: made in the image of God and therefore carry intrinsic worth) cannot be justified through a "healthy" economy (our western perception turns a blind eye to the injustice done to the worlds poorest citizens in the bid to build our "healthy" economy).
Was he a bloodthirsty despot or nation builder? Both? Were his economic achievements tarnished by corruption and human rights abuses? Were there any lasting economic achievements to balance against the reported human rights abuses?
Here are some links covering the developing story:
And for general interest about Soeharto, the Wikipedia entry.