Well... finally achieved an "unprofessional" way to do this, but at least i don't have to edit core files and can handle internal links like i need.
I'm using custom bbcodes to handle internal links. In this way i can evade the rel="nofollow" tag. The unique possible issue is that someone guess the custom bbcode and use it to add spam. Not sure if exists any way to add rights to bbcodes and who can use them.
Also note that this is a temporal fix, and when this issue will be fixed i can run a search-and-replace SQL query to delete all custom bbcode.
Maybe this can also help other webmasters searching for a solution.
