I've got an e90 with bluetooth/no iDrive. Using the home button to activate siri results in siri popping up, a moment (1.5, maybe 2 seconds) of delay while the phone brings up the handsfree interface with the car, then siri audio in/out routes over the handsfree (so using the car speakers and mic, regardless of whether the phone's plugged in via aux). Assuming you've got your phone and car properly paired, this should always be the case - I think siri always uses a handsfree device if one is connected, and I don't think you can set it otherwise (just looked on my own phone to see).
If that's not happening for you, but calls work fine, that seems odd. In settings>bluetooth, what devices are paired? Try "forget this device" for all of them, then re-pair the car and try again.