Are you a Swedish redhead, by any chance?
This would, I feel, fully cement misc. skills into the background of your character, as it would remove the desire to time misc. skill purchases with the 'real' increases you have made with your major attribute gains in order to max out the level up bonuses. It would completely remove them from consideration in the levelling process altogether.
Alternatively, wouldn't doing this alone (making misc. skills not affect attribute growth bonuses at level up) achieve much the same thing as your're attempting to do here, but without removing the 'natural' misc. skill increase through usage a number of people are used to and expect (although, personally, I'm a great fan of restricting it to trainers, as as you pointed out it greatly increases the importance of the choices made selecting major/minor skills at the start of the game, makes levelling and your characters personal narrative far more focused, while adding far greater depth and meaning to the trainer mechanics for those players who (optionally) wish to engage in it. As they might as a viable new and useful cash sink. Of course, a balance between these could be found).
I'm not sure if this is a possible/ completely crap/ broken and utterly useless suggestion, but I thought I'd just throw it out there, for what it's worth.
Edit: Although, now that I think about it, this might be too restrictive, as paying for these misc. skills might be one of the few opportunities certain characters have to increase an attribute that their major/minor set does not naturally cater for well. Ach well.
As you went back and pointed out yourself, it is somewhat necessary to keep misc skills tied to attribute multipliers (which is good, because to answer your other question, it's not possible to stop them from contributing to multipliers in the CS).
It should be noted that stopping the natural experience gain for misc skills does make raising your attributes more difficult, because any attribute multipliers beyond the 10 you get from major/minor skill gains you will have to pay for. Secondly, any attribute that doesn't govern any of your major or minor skills cannot be raised through any *other* means than paying for it, which hopefully should do a lot to help a character's attributes be more reflective of their character type as their misc skill levels are.