Ikailo and all,
I have just been through exactly this situation and would like to help formulate a solution. The issue stems from the fact that there is only one .htaccess file for the whole wordpress installation (in the main wordpress directory) and that .htaccess file is therefore used when rewriting URLs for ALL blogs in the hive.
If you have ANY blogs that use friendly style permalinks then wordpress writes a section of code into the .htaccess file to rewrite those friendly URLs. It does this when you CHANGE the permalink settings
The trouble arises when you install a new blog into the hive - the default permalink setting is to use query string ('?') style permalinks - and installing the new blog REMOVES that section of code from the .htaccess file.
The workaround that I used is, immediately after installing a new blog into the hive, go to ANY settings/permalinks page and resave the settings to use friendly permalinks - that reinstates the code in .htaccess (as far as I can see, it's the same code for ANY permalink rewriting).
But, I agree this is a pain as it stands - and presents a high risk of seriously breaking the whole hive if you forget to do it. The first I noticed it was after installing my second blog the whole of the first blog was broken - minor panic set in until I figured it out.
One way to prevent the hive wipeout scenario is to set the perms on .htaccess to read-only (a good idea in general) once you've set up the first blog with friendly permalinks. Subsequent blog installations will complain about not being able to write .htaccess, but that can be ignored.
So, Ikailo, did you have an idea of how to approach this more generically? If so, maybe I can help out by experimenting?