The problem, as I see it, isn't limited to disabling pihole. I noticed the delay (DNS resolution unavailable) when trying to get acquainted with group management. In the group management documentation, it says you need to enter the command pihole restartdns reload-lists, whenever changing things in group management. I never assumed this could affect other pihole features, such as disabling pihole, so I requested to add code, already available in the sources, to display a warning (count down), whenever this delay occurred.
You can read my request here, unfortunately, nobody confirmed the delay. You still might want to add a comment in the topic, this to ensure that you get at least a warning (on the console, if possible in the web interface), in case the problem cannot be resolved entirely (I'm hoping for a performance improvement, but don't know if this is possible).
Off topic:
I haven't been using pihole disable for a long time, since the feature (disabling / enabling pihole) is applied to pihole and thus to ALL clients.
In pihole v.4.3.2, disabling pihole resulted in simply commenting out the gravity list in /etc/dnsmasq.d/01-pihole.conf and inform pihole-FTL.
In pihole beta5, it looks like this is achieved (NOT TESTED) by changing the variable BLOCKING_ENABLED=true and inform pihole-FTL.
Both solutions result in a delay, practically unnoticeable in v4.3.2, aparentlly very much noticeable in beta5.
To overcome this problem (impact on ALL clients), I searched and found a solution for Windows devices.
My solution is explained here, it assumes using unbound, thus avoiding having to go outside the LAN for DNS resolutions.
Note that the solution (the windows command script) can be used without unbound, by simply using an other resolver (208.67.222.222 - OpenDNS). I even implemented (NOT explained in the topic, explained here) running the script, without having the UAC prompt every time.
The down side of this solution: you have to install the script + desktop shortcut on each windows device you want to give the option.