Yes, a native speaker would say "We've been speaking for 15 minutes". This is the only correct way to say this.
And no, a native speaker would not use a present continuous - this is a classic non-native learner's error.
With time references covering a period of recent time ( for 15 minutes = since 9 o'clock), when the action is still ongoing or has only just stopped, you have to use a present perfect. The present tense is NOT possible.