Seems you explained it pretty well.
Personally, unless you were to just abandon using folders and put everything into one single folder I'm not sure you will manage to work past it.
Even if you were to somehow manage to obfuscate the link, I would think the end user would still be able to just right-click the topic and determine the path.
I suppose one way you might be able to come close would be to just have some topics in the root where the Context Sensitive calls land. Then have inline frames inside those topics that would present the "real" topics.
Perhaps others have better ideas.
We are using a special parameter "base help url" in our tool containing the complete path. The individual menues then only contain the file name of the help file and possibly the name of the subfolder they are stored in.
Example: the base help URL is: C:\Users\Documents\Test_Merge\!SSL!\Responsive_HTML5\mergedProjects\Test Tooltips\
The help path added for the menu that shall be opened context-sensitive is: template\first_topic
I'm not a developer, so I cannot tell you more details about how exactly this procedure is accomplished, but maybe this is an idea you would like to discuss with your colleagues.
Maybe this helps.