Think they've come a long way in the provisioning department. My response here probably does not add a whole lot to resolving your problem but I'm hope at the very least allay some of your fears around managing the system.
As stated not everything is great, especially ACD users.
With Flow through provisioning, getting users configured with all the relevant services is pretty slick in my opinion. room for improvement as is always the case.
The notion around 60-90 minutes to setup two users due to the inherent cumbersome process involved is not accurate at all. The issue is probably more around experience and exposure. My guess is you likely wouldn't feel this way if all the pieces are aligned, properly.
Vince has highlighted the process. notwithstanding that there is some background things that need to be configured first (alignment of the pieces as stated earlier) but this is typically a tech or engineer's competence so they should have done this already.
Things do get more tricky in a Multi MiCollab setup and multicluster setup but I don't think this is your issue. Certificate, firewall and inherent network architecture challenges also add to this but it's par for course.
Think they can definitely improve the way MiCollab does the delete feature especially in a scenario like yours where the user was still logged in. that does cause a lot of headaches. To avoid this, make sure the user is logged out first
I can say with relative certainty that user provisioning is a focus area in the dev cycles for the portfolio.
All the best