If you're in 6.3 OR above, you can update props.conf from Settings->Source types (for sourcetype definitation) OR Settings-> Fields (for field extractionos/transformation).
Inputs.conf can be update (indirectly) from UI Settings->Data Inputs, for regular properties. The advanced properties should be updated only by Splunk Administrators who have in-depth knowledge about those properties, hence they are not exposed via UI.
AFAIK, there is no native option to update the conf file directly. From many activities in Splunk Web, the conf files will get update, so what all conf files/entries you're looking to update from Splunk Web?