I think you totally should encourage your wife to play with her clit during sex! I think a lot of women have somehow decided they can only get off one way, and so stop expierementing with other positions that might feel really good/get them off. Encourage some creatvity!
As to your question, yes, I do rub my clit during sex, not necessarily to have an orgasm, but because it feels good and adds to the overall stimulation during sex. I have been gifted by the orgasm goddess, and can have about five different types of orgasm, one kind being the kind where I rub my clit while having intercourse. I think a lot of women don't realize they're cumming because they're used to having an orgasm only one way- I was like this for a long time before I realized that there are different types of orgasm.
Have fun expierementing!
__________________
Sage knows our mythic history, King Arthur's and Sir Caradoc's
She answers hard acrostics, has a pretty taste for paradox
She quotes in elegiacs all the crimes of Heliogabalus
In conics she can floor peculiarities parabolous
-C'hi