@minrk, after you added the (necessary) dialog for closing the whole Qt console, I realized we forgot to take one case into consideration: leaving any open kernels alone. That comes up when, for example, closing a console that was opened from a notebook via %qtconsole. I think the close dialog should have the same question as now, but offer in addition to 'yes, quit everything' and 'cancel', a 'leave all kernels running' option.
You can no longer leave kernels started by the qtconsole running (it was already much too complicated before there could be n kernels and m tabs, and now it's just not sensible). Quitting the qtconsole should not close kernels it didn't start (it certainly doesn't for me). The message should just clarify that the 'stop all kernels' only refers to kernels that the qtconsole itself started.
Ah, OK. Then yes, just the message needs fixing; right now it sounds like it will nuke every kernel (that's what got me worried).
clarify close dialog on qtconsole
Notes that kernels not started by the qtconsole will not be affected,
and has singular message rather than 'all tabs' when only one tab