It would cast the Council in poor light if they really believed the Ba'ku were indigenous - it just isn't plausible for a planet to support one isolated village of people at comfortable iron age level, and then no other presence of this sapient species. So I'd also like to assume everybody knew what Dougherty did: that these were colonists who had chosen this lifestyle and were not a protected culture in terms of being "virgin" to interstellar influences.
The Council may have been lied to as concerns the exact state of the colonists' abandoning of high tech. The Ba'ku we saw would probably have immediately recognized the holo-fakery, not having "regressed" enough to forget about such tech. Oh, Anij was impressed by the holovillage, but I doubt the entire population could have been kept satisfied for the entire journey. The Son'a plan all along probably was for some unfortunate accident to happen with the holoship so that all the Ba'ku would die as painfully as possible...
There would be other ways to lose such virginity, though: the Capellans in TOS weren't indicated to be colonists, but they were nevertheless contacted for their resources, apparently because they had already been contacted by others (Klingons and possibly more).
Timo Saloniemi