Good questions
Answering your first question:
A strong impact just translates into a strong impact. The aim is to compare impacts and the sum of impacts in comparison to other impacts. For your purpose, though, you do not want to compare impacts, but track one impact along the cause chain. Simply set the weight of the impact to 100 percent and then you will get the result you expect. Rain would then have the same impact as the sediments of the upper level.
However, the sediments shouldn't have less impact than the rain. If the sediments could be prevented rain wouldn't be a problem anymore, would it?
Your second question:
That's a limit to a qualitative model. A factor can be named "Happiness" and then it could mean more or less happiness, but in cannot become sadness. Sometimes it is useful to add an explicit second factor, so that e.g. stress on the job leads to less happiness in the short run while it could lead to sadness in the long run (which is indicated by the long term effect set in the connection's properties).
Does that help?
Happy modeling
Kai