I understand there is a Domino ini setting for turning off all FT-indexing for an entire server. But is there any way to do this for only some databases on the sever, possibly on a per folder basis?
A fulltext can only be created by a user with manager access to the database. In a well configured environment NO USER needs manager access to ANY database.
Even administrators don't need that (as there is Full Administration Mode).
So: Give users editor to the databases, manage access to databases with groups (user managed groups if you want), and then decide which databases to index.
In the end give the rules about which databases should have an index to the admins...