I understand your point but I think it's some steps beyond the scope of such an app. First goal should be to smoothly wake up the user. In addition to the analyse of sleep this can be done by playing some suitable music in the morning but in the end this is the user's choice if and what kind of music he wants to hear in the morning.
But when I select music to wake me up I usually choose one that is able to make me awake. If I'm such a deep sleeper or if I know that I have only few hours to sleep and urgently need to get up by time I always can choose evilalarm as external program. Or I can script a wakeup procedure by myself like first playing a smooth song then calling evilalarm.
Second argument: when a user already stopped music and logging he could be considered to be awake. So there'd be no need to let the alarm in queue.

To make it short: my opinion is that I'd like to have the choice to get up by music or alarm or anything else. So I would appreciate if alarm gets deleted from queue when user stops current logging. And additionally it would be fine to have the choice to enable or disable alarm at all.

But as this point is now cleared (e.g.: by design) I can now vote for current version!