Either they were just taking advantage of an opportunity that presented itself or they completely mind raped Revan. The latter I find to be questionable ethics on the Jedi Council's part.
What happened to Revan's mind wasn't changed. His brain got ****ed up when Malak betrayed him (having a landmine go off under your feet can do that to ya). If Kreia does indeed say that the Jedi Council mind-wiped Revan (I don't recall when or where she ever says this in the game. As far as I know, she hardly at all talks about what happens to him between his capture and Malak's Death), then the obvious explanation is that either she's making an assumption (since she sure as hell wasn't present for any of those events) or ignoring the facts because she's a Revan fangirl. Regardless of whether Kreia believes she's telling the truth about this matter (again, assuming that she says anything about it at all), the fact of the matter is that it's the word of Kreia, who was not there, against the word of Bastila and the other Jedi, who were
"There is something going on in time and space, and beyond time and space, which, whether we like it or not, spells duty." -Winston Churchill
"For of all sad words of tongue or pen, The saddest are these: 'It might have been!'" -John Whittier
"Apathy is death." -Kreia