I wouldn't force the issue. Instead, I would write down the date and description of how the house-rule was used, and then be sure to use that myself as a player. The only time I would be troubled would be if, when I use the house-rule to my advantage, the DM objected. At that point, I might explain how he used it and see if he was interested in being fair about it. If he allowed its use, then great. If not, then I have a choice to make. Do I stay in a campaign where the DM can break an established rule, but I cannot?
Note that I am often on board for various explanations of exceptions to rules. For example, if the DM explained that his character was able to threaten because of a special feat, then I would be perfectly willing to let it slide... although I would want to look into acquiring the feat. If that stuff seems possible, then why object?
My favorite type of player/DM interaction is when I see a player making a bad character build and so I pit them against someone similar but with a good character build. My players have repeatedly decided to revise their own characters (or start over from scratch) in order to take advantage of abilities that I used effectively in play. I don't think players typically object to enemies who are legitimately better -- they only object when the enemies get to cheat physics or laws of the universe. I'd do my best to be sure about what in fact happened in your case. Does the DM really think spellcasters threaten, or did the spellcaster have a feat or variant ability? Whatever the case, it only breaks down if the DM gives a cheaty advantage to his NPCs that you are barred from using. Otherwise, it's all good. (In my opinion, of course.)