As per usual, I think you're missing the point, Steve.
It's not that the movies are retconning the comics. I fully understand and support that certain things must be adapted when changing the medium (which is also why I have no gripes with the way Halo: Reach changed canon from the Fall of Reach; the original medium supersedes secondary media for canon anyway, though). I didn't have a problem with the way they changed Havok from the comics to be much younger that Cyclops. Also in regards to your comment about different comic book story lines, Marvel is pretty good about that. It's all convoluted, sure, but unless they explicitly recognize it as a reboot (like the Ultimate universe), it's all part of the Marvel multi-verse. While complicated, it does all have a single storyline. At least as I understand it. And either way, Marvel comics have been going for 70 bleeding years. These are only five movies. It's hardly comparable in the sheer volume of content.
The problem isn't that the X-Men movies and the X-Men comics have different canons. That's fine and, quite frankly, to be expected. The problem is that both X-Men: First Class and X-Men Origins: Wolverine have a number of continuity errors with X1-3. This, in and of itself, is not necessarily a bad thing, except that both First Class and Origins: Wolverine have masqueraded as prequels. While Origins: Wolverine is the far more blatant offender, it's still annoying.
Some of the decisions which they've made which have caused these continuity errors are not well justified. Emma Frost's characterization in First Class is almost forgivable because she has such a large role to play as a main antagonist to Charles, but many of the others do not serve a large enough purpose to be so easily excused. I know I'm nitpicking on a lot of the things, but quite frankly it's just lazy. If they wanted more freedom to disregard things from X1-3, they should have just gone full-on reboot instead of this awkward middle ground. It's sloppy writing, and I can't abide sloppy writing.