OK, there are some strange things happening with my phone.

I commented out the line 63 in wifi.sh:
# print_msg "WLAN DISABLED" "OK"
and that works as expected.

But after some more testing, with and without the pop-up, my phone reboots after disabling wifi, regardless of any other application.
Another problem is that after the reboot, in 4 out of 5 times, the file wifi.sh is totally empty so I have to reinstall wifi-switcher.

I would say that it looks like the phone doesn't like fast wifi enabled/disabled cycles (~10 seconds between enabling and disabling).
Or maybe this is just something with my phone, can anyone else repeat this behavior?

Anyway, thanks for your help. If you have any idea why this is happening, I would be grateful.

EDIT: well, now my phone rebooted after disabling wlan after I have used the wifi for ~30 minutes...