Moral philosophers will disagree on this topic; there are many different theories of moral worth. Some place significant weight on intentions, some do not. I think one helpful way of approaching this issue is to sort out the different considerations at stake. First, consider the act. We can understand the act as it is embedded in the particular circumstance, or the act as it is itself. For example, there is something that is always bad about the act of killing. Yet, killing in wartime is (at least) not always bad. Viewing the act of killing as it is embedded in the circumstance of warfare changes the moral evaluation of the act. Second,consider the agent. We can imagine all sorts of circumstances where "a good person does a bad thing". A person harms someone by accident; a person tries to help someone yet fails miserably through no fault of her own. These are cases where intention and acts come apart.

These considerations might help to explain some of the examples you raise in your question. Take the case of suffering. I think we can go ahead and say that suffering in itself is bad. Yet, as you note, we wouldn't necessarily want to say that someone is wrong or sinful for suffering. It could be the case that someone is suffering through no fault of her own, in which case she should not be blamed for suffering. Yet, just because the person cannot be blamed for suffering, doesn't imply that suffering is good: suffering, again considered on its own, is still bad. Bad things can happen to good people - yet to make sense of this we have to isolate the intention, and our evaluation of the agent, from the act, and our evaluation of the act.